Codex is one of the most powerful AI agents for research work. But...
Mushtaq Bilal, PhD@MushtaqBilalPhD
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Apr 20, 2026
~3 min read
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Codex is one of the most powerful AI agents for research work.
But most academics don't know how to get started on it. They're still stuck with ChatGPT.
Here's a step-by-step tutorial to help you get started on Codex.
Codex 101 for academics:
But most academics don't know how to get started on it. They're still stuck with ChatGPT.
Here's a step-by-step tutorial to help you get started on Codex.
Codex 101 for academics:
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1. Go to openai[.]com/codex
Download and instal the Codex app on you computer.
Unlike ChatGPT that you use in your browser, Codex is a desktop app.
Don't be intimidated by its name. You don't need any coding experience to use it.
Download and instal the Codex app on you computer.
Unlike ChatGPT that you use in your browser, Codex is a desktop app.
Don't be intimidated by its name. You don't need any coding experience to use it.
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2. When you open it for the first time, it will create a folder "Playground" on your computer.
Everything you do here will be saved in Playground. You can, of course, change the folder.
For serious academic work, choose the lastes model (GPT-5.4) with "Extra High" Reasoning
Everything you do here will be saved in Playground. You can, of course, change the folder.
For serious academic work, choose the lastes model (GPT-5.4) with "Extra High" Reasoning
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3. When you install Codex, it creates a .codex folder on your computer.
In this folder, there is a subfolder called "skills" and a text file called "AGENTS md."
The AGENTS file is set of governing instructions that Codex will follow every time you ask it do something.
In this folder, there is a subfolder called "skills" and a text file called "AGENTS md."
The AGENTS file is set of governing instructions that Codex will follow every time you ask it do something.
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4. In Playgroud, tell Codex a bit about yourself and the kind of research you.
Be brief. You don't need to write an eassy.
Then ask Codex to create an AGENTS md file based on above details.
And ask it to put the file in the main .codex folder.
Be brief. You don't need to write an eassy.
Then ask Codex to create an AGENTS md file based on above details.
And ask it to put the file in the main .codex folder.
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5. Once it's done, you can see the contents of the file.
If you want to edit the file, go to the .codex folder and open AGENTS in notepad.
Add/edit however you want.
Since it's in your main .codex folder, the instructions are global.
Codex will follow them across projects.
If you want to edit the file, go to the .codex folder and open AGENTS in notepad.
Add/edit however you want.
Since it's in your main .codex folder, the instructions are global.
Codex will follow them across projects.
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6. You can create an AGENTS file within a specific project too.
Creat a folder for a new project on your computer.
Click on the folder icon in front of "Projects." Navigate to the folder you just created.
Ask Codex to create an AGENTS file based on what your project is about.
Creat a folder for a new project on your computer.
Click on the folder icon in front of "Projects." Navigate to the folder you just created.
Ask Codex to create an AGENTS file based on what your project is about.
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7. What makes Codex powerful and versatile is "Skills."
A Skill is a set of instructions for a specific workflow, e.g. brainstorming, synthesizing literature, etc.
Think of a repetitive task you do often (e.g. data extraction).
Ask Codex to create a Skill for that task.
A Skill is a set of instructions for a specific workflow, e.g. brainstorming, synthesizing literature, etc.
Think of a repetitive task you do often (e.g. data extraction).
Ask Codex to create a Skill for that task.
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8. Codex will create a Skill for that task and place in the skills subfolder I mentioned earlier.
Go to skills folder and open the folder of the skill you created.
Within the folder, open SKILL md file.
Just like the AGENTS file, you can edit it if you want to.
Go to skills folder and open the folder of the skill you created.
Within the folder, open SKILL md file.
Just like the AGENTS file, you can edit it if you want to.
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9. To invoke a skill, type in the dollar sign ($) and it will show all the skills you have in Codex.
Select the skill you created and give it a task relevant to that skill.
Evaluate its output, and if you're not satisfied, amend the relevant SKILL file.
Select the skill you created and give it a task relevant to that skill.
Evaluate its output, and if you're not satisfied, amend the relevant SKILL file.
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In summary:
1. Download Codex
2. Create an AGENTS file
3. Create a SKILL
4. Test them both
5. Iterate
1. Download Codex
2. Create an AGENTS file
3. Create a SKILL
4. Test them both
5. Iterate
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If you'd prefer an app that's designed for academic research, check out Chat Academia.
It's a one-stop solution for all your research needs.
15 AI agents integrated with 7 academic databases and 500M+ articles.
Check it out for free:
chatacademia.com
It's a one-stop solution for all your research needs.
15 AI agents integrated with 7 academic databases and 500M+ articles.
Check it out for free:
chatacademia.com
