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 :)
Read original post here
More on Productivity
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Time for hobbies.
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Meditation.
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Headspace helps with the habit.
Here's a meditation guide.
Sit comfortably
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Here's a beginner's video:
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Recap
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Thus, the morning is ideal for your hardest chores.
It makes sense to do these things during your peak performance hours.
Additionally, your morning sets the tone for the day. According to Brian Tracy, the first hour of the workday steers the remainder.
After doing your most critical chores, you may feel accomplished, confident, and motivated for the remainder of the day, which boosts productivity.
Develop Your Essentialism
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You'll either burn out, be spread too thin, or compromise your ideals.
Greg McKeown advises Essentialism:
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According to Greg McKeown, Essentialists live by design, not default.
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#3: Practice saying "no"
If a request or demand conflicts with your aims or principles, you must learn to say no.
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Place Sleep Above All Else
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A productive day starts with a good night's sleep.
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The woman
3 years ago
I received a $2k bribe to replace another developer in an interview
I can't believe they’d even think it works!
Developers are usually interviewed before being hired, right? Every organization wants candidates who meet their needs. But they also want to avoid fraud.
There are cheaters in every field. Only two come to mind for the hiring process:
Lying on a resume.
Cheating on an online test.
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The specifics
My ex-colleague recently texted me. No one from your former office will ever approach you after a year unless they need something.
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What followed surprised me. She'd ask to turn off the camera, he said.
I asked why.
He told me if an applicant is unwell, the interviewer may consider an off-camera interview. His wife will say she's sick and prefers no camera.
The plan left me speechless. I declined politely. He insisted and promised $2k if she got the job.
I felt insulted and told him if he persisted, I'd inform his office. I was furious. Later, I apologized and told him to stop.
I'm not sure what they did after that
I'm not sure if they found someone or listened to me. They probably didn't. How would she do the job if she even got it?
It's an internship, he said. With great pay, though. What should an intern do?
I suggested she do the interview alone. Even if she failed, she'd gain confidence and valuable experience.
Conclusion
Many interviewees cheat. My profession is vital to me, thus I'd rather improve my abilities and apply honestly. It's part of my identity.
Am I truthful? Most professionals are not. They fabricate their CVs. Often.
When you support interview cheating, you encourage more cheating! When someone cheats, another qualified candidate may not obtain the job.
One day, that could be you or me.
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Payouts to founders at IPO
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Coinbase, Uber, UI Path. Uber, Zoom, Spotify, UI Path, and Coinbase founders raised billions. Zoom's founder owned 19% and Spotify's 28% and 13%. Brian Armstrong controlled 20% of Coinbase at IPO and was worth $15bn. Preserving as much equity as possible by staying cash-efficient or raising at high valuations also helps.
The smallest was Ping. Ping's compensation was the smallest. Andre Duand owned 2% but was worth $20m at IPO. That's less than some billion-dollar paydays, but still good.
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William Brucee
3 years ago
This person is probably Satoshi Nakamoto.
Who founded bitcoin is the biggest mystery in technology today, not how it works.
On October 31, 2008, Satoshi Nakamoto posted a whitepaper to a cryptography email list. Still confused by the mastermind who changed monetary history.
Journalists and bloggers have tried in vain to uncover bitcoin's creator. Some candidates self-nominated. We're still looking for the mystery's perpetrator because none of them have provided proof.
One person. I'm confident he invented bitcoin. Let's assess Satoshi Nakamoto before I reveal my pick. Or what he wants us to know.
Satoshi's P2P Foundation biography says he was born in 1975. He doesn't sound or look Japanese. First, he wrote the whitepaper and subsequent articles in flawless English. His sleeping habits are unusual for a Japanese person.
Stefan Thomas, a Bitcoin Forum member, displayed Satoshi's posting timestamps. Satoshi Nakamoto didn't publish between 2 and 8 p.m., Japanese time. Satoshi's identity may not be real.
Why would he disguise himself?
There is a legitimate explanation for this
Phil Zimmermann created PGP to give dissidents an open channel of communication, like Pretty Good Privacy. US government seized this technology after realizing its potential. Police investigate PGP and Zimmermann.
This technology let only two people speak privately. Bitcoin technology makes it possible to send money for free without a bank or other intermediary, removing it from government control.
How much do we know about the person who invented bitcoin?
Here's what we know about Satoshi Nakamoto now that I've covered my doubts about his personality.
Satoshi Nakamoto first appeared with a whitepaper on metzdowd.com. On Halloween 2008, he presented a nine-page paper on a new peer-to-peer electronic monetary system.
Using the nickname satoshi, he created the bitcointalk forum. He kept developing bitcoin and created bitcoin.org. Satoshi mined the genesis block on January 3, 2009.
Satoshi Nakamoto worked with programmers in 2010 to change bitcoin's protocol. He engaged with the bitcoin community. Then he gave Gavin Andresen the keys and codes and transferred community domains. By 2010, he'd abandoned the project.
The bitcoin creator posted his goodbye on April 23, 2011. Mike Hearn asked Satoshi if he planned to rejoin the group.
“I’ve moved on to other things. It’s in good hands with Gavin and everyone.”
Nakamoto Satoshi
The man who broke the banking system vanished. Why?
Satoshi's wallets held 1,000,000 BTC. In December 2017, when the price peaked, he had over US$19 billion. Nakamoto had the 44th-highest net worth then. He's never cashed a bitcoin.
This data suggests something happened to bitcoin's creator. I think Hal Finney is Satoshi Nakamoto .
Hal Finney had ALS and died in 2014. I suppose he created the future of money, then he died, leaving us with only rumors about his identity.
Hal Finney, who was he?
Hal Finney graduated from Caltech in 1979. Student peers voted him the smartest. He took a doctoral-level gravitational field theory course as a freshman. Finney's intelligence meets the first requirement for becoming Satoshi Nakamoto.
Students remember Finney holding an Ayn Rand book. If he'd read this, he may have developed libertarian views.
His beliefs led him to a small group of freethinking programmers. In the 1990s, he joined Cypherpunks. This action promoted the use of strong cryptography and privacy-enhancing technologies for social and political change. Finney helped them achieve a crypto-anarchist perspective as self-proclaimed privacy defenders.
Zimmermann knew Finney well.
Hal replied to a Cypherpunk message about Phil Zimmermann and PGP. He contacted Phil and became PGP Corporation's first member, retiring in 2011. Satoshi Nakamoto quit bitcoin in 2011.
Finney improved the new PGP protocol, but he had to do so secretly. He knew about Phil's PGP issues. I understand why he wanted to hide his identity while creating bitcoin.
Why did he pretend to be from Japan?
His envisioned persona was spot-on. He resided near scientist Dorian Prentice Satoshi Nakamoto. Finney could've assumed Nakamoto's identity to hide his. Temple City has 36,000 people, so what are the chances they both lived there? A cryptographic genius with the same name as Bitcoin's creator: coincidence?
Things went differently, I think.
I think Hal Finney sent himself Satoshis messages. I know it's odd. If you want to conceal your involvement, do as follows. He faked messages and transferred the first bitcoins to himself to test the transaction mechanism, so he never returned their money.
Hal Finney created the first reusable proof-of-work system. The bitcoin protocol. In the 1990s, Finney was intrigued by digital money. He invented CRypto cASH in 1993.
Legacy
Hal Finney's contributions should not be forgotten. Even if I'm wrong and he's not Satoshi Nakamoto, we shouldn't forget his bitcoin contribution. He helped us achieve a better future.
Nick Babich
2 years ago
Is ChatGPT Capable of Generating a Complete Mobile App?
TL;DR: It'll be harder than you think.
Mobile app development is a complicated product design sector. You require broad expertise to create a mobile app. You must write Swift or Java code and consider mobile interactions.
When ChatGPT was released, many were amazed by its capabilities and wondered if it could replace designers and developers. This article will use ChatGPT to answer a specific query.
Can ChatGPT build an entire iOS app?
This post will use ChatGPT to construct an iOS meditation app. Video of the article is available.
App concepts for meditation
After deciding on an app, think about the user experience. What should the app offer?
Let's ask ChatGPT for the answer.
ChatGPT described a solid meditation app with various exercises. Use this list to plan product design. Our first product iteration will have few features. A simple, one-screen software will let users set the timeframe and play music during meditation.
Structure of information
Information architecture underpins product design. Our app's navigation mechanism should be founded on strong information architecture, so we need to identify our mobile's screens first.
ChatGPT can define our future app's information architecture since we already know it.
ChatGPT uses the more complicated product's structure. When adding features to future versions of our product, keep this information picture in mind.
Color palette
Meditation apps need colors. We want to employ relaxing colors in a meditation app because colors affect how we perceive items. ChatGPT can suggest product colors.
See the hues in person:
Neutral colors dominate the color scheme. Playing with color opacity makes this scheme useful.
Ambiance music
Meditation involves music. Well-chosen music calms the user.
Let ChatGPT make music for us.
ChatGPT can only generate text. It directs us to Spotify or YouTube to look for such stuff and makes precise recommendations.
Fonts
Fonts can impress app users. Round fonts are easier on the eyes and make a meditation app look friendlier.
ChatGPT can suggest app typefaces. I compare two font pairs when making a product. I'll ask ChatGPT for two font pairs.
See the hues in person:
Despite ChatGPT's convincing font pairing arguments, the output is unattractive. The initial combo (Open Sans + Playfair Display) doesn't seem to work well for a mediation app.
Content
Meditation requires the script. Find the correct words and read them calmly and soothingly to help listeners relax and focus on each region of their body to enhance the exercise's effect.
ChatGPT's offerings:
ChatGPT outputs code. My prompt's word script may cause it.
Timer
After fonts, colors, and content, construct functional pieces. Timer is our first functional piece. The meditation will be timed.
Let ChatGPT write Swift timer code (since were building an iOS app, we need to do it using Swift language).
ChatGPT supplied a timer class, initializer, and usage guidelines.
Apple Xcode requires a playground to test this code. Xcode will report issues after we paste the code to the playground.
Fixing them is simple. Just change Timer to another class name (Xcode shows errors because it thinks that we access the properties of the class we’ve created rather than the system class Timer; it happens because both classes have the same name Timer). I titled our class Timero and implemented the project. After this quick patch, ChatGPT's code works.
Can ChatGPT produce a complete app?
Since ChatGPT can help us construct app components, we may question if it can write a full app in one go.
Question ChatGPT:
ChatGPT supplied basic code and instructions. It's unclear if ChatGPT purposely limits output or if my prompt wasn't good enough, but the tool cannot produce an entire app from a single prompt.
However, we can contact ChatGPT for thorough Swift app construction instructions.
We can ask ChatGPT for step-by-step instructions now that we know what to do. Request a basic app layout from ChatGPT.
Copying this code to an Xcode project generates a functioning layout.
Takeaways
ChatGPT may provide step-by-step instructions on how to develop an app for a specific system, and individual steps can be utilized as prompts to ChatGPT. ChatGPT cannot generate the source code for the full program in one go.
The output that ChatGPT produces needs to be examined by a human. The majority of the time, you will need to polish or adjust ChatGPT's output, whether you develop a color scheme or a layout for the iOS app.
ChatGPT is unable to produce media material. Although ChatGPT cannot be used to produce images or sounds, it can assist you build prompts for programs like midjourney or Dalle-2 so that they can provide the appropriate images for you.