More on Science
Daniel Clery
3 years ago
Twisted device investigates fusion alternatives
German stellarator revamped to run longer, hotter, compete with tokamaks
Tokamaks have dominated the search for fusion energy for decades. Just as ITER, the world's largest and most expensive tokamak, nears completion in southern France, a smaller, twistier testbed will start up in Germany.
If the 16-meter-wide stellarator can match or outperform similar-size tokamaks, fusion experts may rethink their future. Stellarators can keep their superhot gases stable enough to fuse nuclei and produce energy. They can theoretically run forever, but tokamaks must pause to reset their magnet coils.
The €1 billion German machine, Wendelstein 7-X (W7-X), is already getting "tokamak-like performance" in short runs, claims plasma physicist David Gates, preventing particles and heat from escaping the superhot gas. If W7-X can go long, "it will be ahead," he says. "Stellarators excel" Eindhoven University of Technology theorist Josefine Proll says, "Stellarators are back in the game." A few of startup companies, including one that Gates is leaving Princeton Plasma Physics Laboratory, are developing their own stellarators.
W7-X has been running at the Max Planck Institute for Plasma Physics (IPP) in Greifswald, Germany, since 2015, albeit only at low power and for brief runs. W7-X's developers took it down and replaced all inner walls and fittings with water-cooled equivalents, allowing for longer, hotter runs. The team reported at a W7-X board meeting last week that the revised plasma vessel has no leaks. It's expected to restart later this month to show if it can get plasma to fusion-igniting conditions.
Wendelstein 7-X's water-cooled inner surface allows for longer runs.
HOSAN/IPP
Both stellarators and tokamaks create magnetic gas cages hot enough to melt metal. Microwaves or particle beams heat. Extreme temperatures create a plasma, a seething mix of separated nuclei and electrons, and cause the nuclei to fuse, releasing energy. A fusion power plant would use deuterium and tritium, which react quickly. Non-energy-generating research machines like W7-X avoid tritium and use hydrogen or deuterium instead.
Tokamaks and stellarators use electromagnetic coils to create plasma-confining magnetic fields. A greater field near the hole causes plasma to drift to the reactor's wall.
Tokamaks control drift by circulating plasma around a ring. Streaming creates a magnetic field that twists and stabilizes ionized plasma. Stellarators employ magnetic coils to twist, not plasma. Once plasma physicists got powerful enough supercomputers, they could optimize stellarator magnets to improve plasma confinement.
W7-X is the first large, optimized stellarator with 50 6- ton superconducting coils. Its construction began in the mid-1990s and cost roughly twice the €550 million originally budgeted.
The wait hasn't disappointed researchers. W7-X director Thomas Klinger: "The machine operated immediately." "It's a friendly machine." It did everything we asked." Tokamaks are prone to "instabilities" (plasma bulging or wobbling) or strong "disruptions," sometimes associated to halted plasma flow. IPP theorist Sophia Henneberg believes stellarators don't employ plasma current, which "removes an entire branch" of instabilities.
In early stellarators, the magnetic field geometry drove slower particles to follow banana-shaped orbits until they collided with other particles and leaked energy. Gates believes W7-X's ability to suppress this effect implies its optimization works.
W7-X loses heat through different forms of turbulence, which push particles toward the wall. Theorists have only lately mastered simulating turbulence. W7-X's forthcoming campaign will test simulations and turbulence-fighting techniques.
A stellarator can run constantly, unlike a tokamak, which pulses. W7-X has run 100 seconds—long by tokamak standards—at low power. The device's uncooled microwave and particle heating systems only produced 11.5 megawatts. The update doubles heating power. High temperature, high plasma density, and extensive runs will test stellarators' fusion power potential. Klinger wants to heat ions to 50 million degrees Celsius for 100 seconds. That would make W7-X "a world-class machine," he argues. The team will push for 30 minutes. "We'll move step-by-step," he says.
W7-X's success has inspired VCs to finance entrepreneurs creating commercial stellarators. Startups must simplify magnet production.
Princeton Stellarators, created by Gates and colleagues this year, has $3 million to build a prototype reactor without W7-X's twisted magnet coils. Instead, it will use a mosaic of 1000 HTS square coils on the plasma vessel's outside. By adjusting each coil's magnetic field, operators can change the applied field's form. Gates: "It moves coil complexity to the control system." The company intends to construct a reactor that can fuse cheap, abundant deuterium to produce neutrons for radioisotopes. If successful, the company will build a reactor.
Renaissance Fusion, situated in Grenoble, France, raised €16 million and wants to coat plasma vessel segments in HTS. Using a laser, engineers will burn off superconductor tracks to carve magnet coils. They want to build a meter-long test segment in 2 years and a full prototype by 2027.
Type One Energy in Madison, Wisconsin, won DOE money to bend HTS cables for stellarator magnets. The business carved twisting grooves in metal with computer-controlled etching equipment to coil cables. David Anderson of the University of Wisconsin, Madison, claims advanced manufacturing technology enables the stellarator.
Anderson said W7-X's next phase will boost stellarator work. “Half-hour discharges are steady-state,” he says. “This is a big deal.”
Sam Warain
3 years ago
Sam Altman, CEO of Open AI, foresees the next trillion-dollar AI company
“I think if I had time to do something else, I would be so excited to go after this company right now.”
Sam Altman, CEO of Open AI, recently discussed AI's present and future.
Open AI is important. They're creating the cyberpunk and sci-fi worlds.
They use the most advanced algorithms and data sets.
GPT-3...sound familiar? Open AI built most copyrighting software. Peppertype, Jasper AI, Rytr. If you've used any, you'll be shocked by the quality.
Open AI isn't only GPT-3. They created DallE-2 and Whisper (a speech recognition software released last week).
What will they do next? What's the next great chance?
Sam Altman, CEO of Open AI, recently gave a lecture about the next trillion-dollar AI opportunity.
Who is the organization behind Open AI?
Open AI first. If you know, skip it.
Open AI is one of the earliest private AI startups. Elon Musk, Greg Brockman, and Rebekah Mercer established OpenAI in December 2015.
OpenAI has helped its citizens and AI since its birth.
They have scary-good algorithms.
Their GPT-3 natural language processing program is excellent.
The algorithm's exponential growth is astounding. GPT-2 came out in November 2019. May 2020 brought GPT-3.
Massive computation and datasets improved the technique in just a year. New York Times said GPT-3 could write like a human.
Same for Dall-E. Dall-E 2 was announced in April 2022. Dall-E 2 won a Colorado art contest.
Open AI's algorithms challenge jobs we thought required human innovation.
So what does Sam Altman think?
The Present Situation and AI's Limitations
During the interview, Sam states that we are still at the tip of the iceberg.
So I think so far, we’ve been in the realm where you can do an incredible copywriting business or you can do an education service or whatever. But I don’t think we’ve yet seen the people go after the trillion dollar take on Google.
He's right that AI can't generate net new human knowledge. It can train and synthesize vast amounts of knowledge, but it simply reproduces human work.
“It’s not going to cure cancer. It’s not going to add to the sum total of human scientific knowledge.”
But the key word is yet.
And that is what I think will turn out to be wrong that most surprises the current experts in the field.
Reinforcing his point that massive innovations are yet to come.
But where?
The Next $1 Trillion AI Company
Sam predicts a bio or genomic breakthrough.
There’s been some promising work in genomics, but stuff on a bench top hasn’t really impacted it. I think that’s going to change. And I think this is one of these areas where there will be these new $100 billion to $1 trillion companies started, and those areas are rare.
Avoid human trials since they take time. Bio-materials or simulators are suitable beginning points.
AI may have a breakthrough. DeepMind, an OpenAI competitor, has developed AlphaFold to predict protein 3D structures.
It could change how we see proteins and their function. AlphaFold could provide fresh understanding into how proteins work and diseases originate by revealing their structure. This could lead to Alzheimer's and cancer treatments. AlphaFold could speed up medication development by revealing how proteins interact with medicines.
Deep Mind offered 200 million protein structures for scientists to download (including sustainability, food insecurity, and neglected diseases).
Being in AI for 4+ years, I'm amazed at the progress. We're past the hype cycle, as evidenced by the collapse of AI startups like C3 AI, and have entered a productive phase.
We'll see innovative enterprises that could replace Google and other trillion-dollar companies.
What happens after AI adoption is scary and unpredictable. How will AGI (Artificial General Intelligence) affect us? Highly autonomous systems that exceed humans at valuable work (Open AI)
My guess is that the things that we’ll have to figure out are how we think about fairly distributing wealth, access to AGI systems, which will be the commodity of the realm, and governance, how we collectively decide what they can do, what they don’t do, things like that. And I think figuring out the answer to those questions is going to just be huge. — Sam Altman CEO
Jamie Ducharme
3 years ago
How monkeypox spreads (and doesn't spread)
Monkeypox was rare until recently. In 2005, a research called a cluster of six monkeypox cases in the Republic of Congo "the longest reported chain to date."
That's changed. This year, over 25,000 monkeypox cases have been reported in 83 countries, indicating widespread human-to-human transmission.
What spreads monkeypox? Monkeypox transmission research is ongoing; findings may change. But science says...
Most cases were formerly animal-related.
According to the WHO, monkeypox was first diagnosed in an infant in the DRC in 1970. After that, instances were infrequent and often tied to animals. In 2003, 47 Americans contracted rabies from pet prairie dogs.
In 2017, Nigeria saw a significant outbreak. NPR reported that doctors diagnosed young guys without animal exposure who had genital sores. Nigerian researchers highlighted the idea of sexual transmission in a 2019 study, but the theory didn't catch on. “People tend to cling on to tradition, and the idea is that monkeypox is transmitted from animals to humans,” explains research co-author Dr. Dimie Ogoina.
Most monkeypox cases are sex-related.
Human-to-human transmission of monkeypox occurs, and sexual activity plays a role.
Joseph Osmundson, a clinical assistant professor of biology at NYU, says most transmission occurs in queer and gay sexual networks through sexual or personal contact.
Monkeypox spreads by skin-to-skin contact, especially with its blister-like rash, explains Ogoina. Researchers are exploring whether people can be asymptomatically contagious, but they are infectious until their rash heals and fresh skin forms, according to the CDC.
A July research in the New England Journal of Medicine reported that of more than 500 monkeypox cases in 16 countries as of June, 95% were linked to sexual activity and 98% were among males who have sex with men. WHO Director-General Tedros Adhanom Ghebreyesus encouraged males to temporarily restrict their number of male partners in July.
Is monkeypox a sexually transmitted infection (STI)?
Skin-to-skin contact can spread monkeypox, not simply sexual activities. Dr. Roy Gulick, infectious disease chief at Weill Cornell Medicine and NewYork-Presbyterian, said monkeypox is not a "typical" STI. Monkeypox isn't a STI, claims the CDC.
Most cases in the current outbreak are tied to male sexual behavior, but Osmundson thinks the virus might also spread on sports teams, in spas, or in college dorms.
Can you get monkeypox from surfaces?
Monkeypox can be spread by touching infected clothing or bedding. According to a study, a U.K. health care worker caught monkeypox in 2018 after handling ill patient's bedding.
Angela Rasmussen, a virologist at the University of Saskatchewan in Canada, believes "incidental" contact seldom distributes the virus. “You need enough virus exposure to get infected,” she says. It's conceivable after sharing a bed or towel with an infectious person, but less likely after touching a doorknob, she says.
Dr. Müge evik, a clinical lecturer in infectious diseases at the University of St. Andrews in Scotland, says there is a "spectrum" of risk connected with monkeypox. "Every exposure isn't equal," she explains. "People must know where to be cautious. Reducing [sexual] partners may be more useful than cleaning coffee shop seats.
Is monkeypox airborne?
Exposure to an infectious person's respiratory fluids can cause monkeypox, but the WHO says it needs close, continuous face-to-face contact. CDC researchers are still examining how often this happens.
Under precise laboratory conditions, scientists have shown that monkeypox can spread via aerosols, or tiny airborne particles. But there's no clear evidence that this is happening in the real world, Rasmussen adds. “This is expanding predominantly in communities of males who have sex with men, which suggests skin-to-skin contact,” she explains. If airborne transmission were frequent, she argues, we'd find more occurrences in other demographics.
In the shadow of COVID-19, people are worried about aerosolized monkeypox. Rasmussen believes the epidemiology is different. Different viruses.
Can kids get monkeypox?
More than 80 youngsters have contracted the virus thus far, mainly through household transmission. CDC says pregnant women can spread the illness to their fetus.
Among the 1970s, monkeypox predominantly affected children, but by the 2010s, it was more common in adults, according to a February study. The study's authors say routine smallpox immunization (which protects against monkeypox) halted when smallpox was eradicated. Only toddlers were born after smallpox vaccination halted decades ago. More people are vulnerable now.
Schools and daycares could become monkeypox hotspots, according to pediatric instances. Ogoina adds this hasn't happened in Nigeria's outbreaks, which is encouraging. He says, "I'm not sure if we should worry." We must be careful and seek evidence.
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Camilla Dudley
3 years ago
How to gain Twitter followers: A 101 Guide
No wonder brands use Twitter to reach their audience. 53% of Twitter users buy new products first.
Twitter growth does more than make your brand look popular. It helps clients trust your business. It boosts your industry standing. It shows clients, prospects, and even competitors you mean business.
How can you naturally gain Twitter followers?
Share useful information
Post visual content
Tweet consistently
Socialize
Spread your @name everywhere.
Use existing customers
Promote followers
Share useful information
Twitter users join conversations and consume material. To build your followers, make sure your material appeals to them and gives value, whether it's sales, product lessons, or current events.
Use Twitter Analytics to learn what your audience likes.
Explore popular topics by utilizing relevant keywords and hashtags. Check out this post on how to use Twitter trends.
Post visual content
97% of Twitter users focus on images, so incorporating media can help your Tweets stand out. Visuals and videos make content more engaging and memorable.
Tweet often
Your audience should expect regular content updates. Plan your ideas and tweet during crucial seasons and events with a content calendar.
Socialize
Twitter connects people. Do more than tweet. Follow industry leaders. Retweet influencers, engage with thought leaders, and reply to mentions and customers to boost engagement.
Micro-influencers can promote your brand or items. They can help you gain new audiences' trust.
Spread your @name everywhere.
Maximize brand exposure. Add a follow button on your website, link to it in your email signature and newsletters, and promote it on business cards or menus.
Use existing customers
Emails can be used to find existing Twitter clients. Upload your email contacts and follow your customers on Twitter to start a dialogue.
Promote followers
Run a followers campaign to boost your organic growth. Followers campaigns promote your account to a particular demographic, and you only pay when someone follows you.
Consider short campaigns to enhance momentum or an always-on campaign to gain new followers.
Increasing your brand's Twitter followers takes effort and experimentation, but the payback is huge.
👋 Follow me on twitter
Entreprogrammer
3 years ago
The Steve Jobs Formula: A Guide to Everything
A must-read for everyone
Jobs is well-known. You probably know the tall, thin guy who wore the same clothing every day. His influence is unavoidable. In fewer than 40 years, Jobs' innovations have impacted computers, movies, cellphones, music, and communication.
Steve Jobs may be more imaginative than the typical person, but if we can use some of his ingenuity, ambition, and good traits, we'll be successful. This essay explains how to follow his guidance and success secrets.
1. Repetition is necessary for success.
Be patient and diligent to master something. Practice makes perfect. This is why older workers are often more skilled.
When should you repeat a task? When you're confident and excited to share your product. It's when to stop tweaking and repeating.
Jobs stated he'd make the crowd sh** their pants with an iChat demo.
Use this in your daily life.
Start with the end in mind. You can put it in writing and be as detailed as you like with your plan's schedule and metrics. For instance, you have a goal of selling three coffee makers in a week.
Break it down, break the goal down into particular tasks you must complete, and then repeat those tasks. To sell your coffee maker, you might need to make 50 phone calls.
Be mindful of the amount of work necessary to produce the desired results. Continue doing this until you are happy with your product.
2. Acquire the ability to add and subtract.
How did Picasso invent cubism? Pablo Picasso was influenced by stylised, non-naturalistic African masks that depict a human figure.
Artists create. Constantly seeking inspiration. They think creatively about random objects. Jobs said creativity is linking things. Creative people feel terrible when asked how they achieved something unique because they didn't do it all. They saw innovation. They had mastered connecting and synthesizing experiences.
Use this in your daily life.
On your phone, there is a note-taking app. Ideas for what you desire to learn should be written down. It may be learning a new language, calligraphy, or anything else that inspires or intrigues you.
Note any ideas you have, quotations, or any information that strikes you as important.
Spend time with smart individuals, that is the most important thing. Jim Rohn, a well-known motivational speaker, has observed that we are the average of the five people with whom we spend the most time.
Learning alone won't get you very far. You need to put what you've learnt into practice. If you don't use your knowledge and skills, they are useless.
3. Develop the ability to refuse.
Steve Jobs deleted thousands of items when he created Apple's design ethic. Saying no to distractions meant upsetting customers and partners.
John Sculley, the former CEO of Apple, said something like this. According to Sculley, Steve’s methodology differs from others as he always believed that the most critical decisions are things you choose not to do.
Use this in your daily life.
Never be afraid to say "no," "I won't," or "I don't want to." Keep it simple. This method works well in some situations.
Give a different option. For instance, X might be interested even if I won't be able to achieve it.
Control your top priority. Before saying yes to anything, make sure your work schedule and priority list are up to date.
4. Follow your passion
“Follow your passion” is the worst advice people can give you. Steve Jobs didn't start Apple because he suddenly loved computers. He wanted to help others attain their maximum potential.
Great things take a lot of work, so quitting makes sense if you're not passionate. Jobs learned from history that successful people were passionate about their work and persisted through challenges.
Use this in your daily life.
Stay away from your passion. Allow it to develop daily. Keep working at your 9-5-hour job while carefully gauging your level of desire and endurance. Less risk exists.
The truth is that if you decide to work on a project by yourself rather than in a group, it will take you years to complete it instead of a week. Instead, network with others who have interests in common.
Prepare a fallback strategy in case things go wrong.
Success, this small two-syllable word eventually gives your life meaning, a perspective. What is success? For most, it's achieving their ambitions. However, there's a catch. Successful people aren't always happy.
Furthermore, where do people’s goals and achievements end? It’s a never-ending process. Success is a journey, not a destination. We wish you not to lose your way on this journey.
Leonardo Castorina
3 years ago
How to Use Obsidian to Boost Research Productivity
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:
- 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.
- Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
- 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
Carl Sagan: “To make an apple pie from scratch, you must first create the universe.”
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:
#Tags and [[Links]] over /Folders/
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.
“Deep stuff Leo,” one person said. So my main issue is basic organization, losing track of my tasks and the reasons for them.
As a result, I'd go on other experiments that didn't make sense, and have to reverse engineer my logic for thesis writing. - PhD student now wise Postdoc
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:
- It had to be private, and nobody had to be able to read the entries.
- 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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