This is a five-part tutorial to help academic researchers get started with Codex.
I have written it in an accessible language, and you don't need any technical background to understand this tutorial or use Codex.
Part 1: What Is Codex?
Codex is a tool that can run on your computer. Don't be intimidated by the word "code." You don't need any coding or programming skills to use it. You install the Codex app on your computer just like you would an app like Zoom or Zotero.
Once you have it on your computer, you open your project folder (dissertation, paper, etc.) and let Codex work inside the folder. Codex can read files in the folder, edit existing files, and create new ones. It can also continue with saved sessions and project instructions when you return to your work.
Unlike browser-based apps like ChatGPT and Gemini that only "talk," Codex can actually "do" things for you.
1.1 Why You Should Care About It?
You are a researcher and have a folder on your computer with several PDFs, drafts of your papers, spreadsheets, datasets, and a few transcripts of interviews. All these documents are relevant to your project, but you need to make connections across published literature, gathered data, and your own notes.
This is the kind of use-case that Codex is useful for.
Most academics and researchers have used AI apps in their browsers (ChatGPT, Claude, Gemini, etc.) You open a tab and type in a prompt and the AI replies. If you want to ask questions about your papers or drafts, you add them to ChatGPT or Claude.
Codex is different because instead of you bringing your files to an AI app in the browser, you bring the AI into the folder containing all your data.
1.2 Why Codex Matters for Academic Work
There are two fundamental ways in which Codex can work as your reliable and powerful research assistant.
First, Codex can follow project instructions about you, your research, your writing style, and your evolving research requirements. You won't have to explain your requirements repeatedly if you put them in a visible instruction file.
Second, since Codex works within a folder on your computer, it can process multiple files at a time. For example, it can go through the PDFs it can read in your folder and extract relevant information (objectives, methodology, etc.) from them. You can even ask it to create a new file based on extracted information.
Codex can work with many types of files from Word files to Excel sheets, PDFs, etc., though scanned or badly formatted files may need extra checking.
1.3 What Does It Mean in Practical Terms?
If you are a qualitative researcher, load a folder full of interview transcripts and ask Codex to give you every instance of a particular utterance, e.g. how each participant talked about a given subject. Then ask it to look for overarching themes across interviews.
If you are a quantitative researcher, add a messy CSV or an Excel sheet in your folder and ask Codex to clean it up for you. You can ask it to run descriptive statistics or ask it to explain a critical comment made by a reviewer.
1.4 What Codex is Not
Codex is an incredibly powerful tool, but it is not a replacement for your expert judgment. It can draft, summarize, code, but what counts as argument or evidence is your responsibility.
Academics who are likely to succeed using Codex are the ones who treat it as a research assistant and not those who outsource all their thinking and judgment to it.
Part 2: Installing Codex App, Your First Session
If you're new to Codex, set aside 15-20 minutes to install it and set it up. You don't need any coding skills to use Codex.
You will need a ChatGPT Plus or Pro plan to use Codex on your computer.
2.1 Installation
The Codex app is available for both Windows and Mac. Go to openai.com/codex and download the version compatible with your computer. Run it the way you would any other installer (e.g. Zoom, Zotero, etc.).
Open the app once you have installed it. The first time you open it, Codex will ask you to sign in through the browser or connect your account. Once you have signed in, you will see a workspace where you can start sessions.
By default, Codex will create a folder in your “Documents” called “Playground.” Everything you do will be done within this folder unless you move to another folder.
2.2 Opening Your First Folder (Project)
Codex treats folders as “Projects.” Except for the names, there is no difference between the two.
For practice, create a folder called “Codex Research Assistant” on your computer. Then click on the “Playground” under the chat bar. From the drop-down menu, select “Add new project” and navigate to the folder you just created.
Now Codex is inside that folder. It has access to the files and subfolders inside the main folder, according to the permissions you give it.
2.3 What a Session Looks Like
A session is the conversation you have with Codex in the main chat panel just like you do it in browser apps like ChatGPT.
The interaction is like browser-based apps like ChatGPT. The only difference is that now Codex has access to your files on your computer. It also has the ability to create files on your computer.
Once you are in the folder, give Codex a simple prompt like:
Read all the papers in the folder and give me their main arguments as a separate file.
That's it. Most of your interaction with Codex would be writing instructions like this.
Codex will go ahead and retrieve relevant information from the papers and start creating a new file. This file will show up in the folder that you are working in.
As it proceeds, it may ask you for permission to do so. You can configure Codex permissions, but in the beginning, it's a good idea to make Codex ask for permissions. You don't want Codex to end up deleting or changing any important files without asking you.
Every session you start in Codex is saved in the app's conversation history.
Part 3: Codex as Your Research Assistant
When Codex starts work in a folder, it looks for a file called AGENTS.md for a set of instructions to follow. Notice the block letters, this is important.
There are two ways you can create an AGENTS.md file: automatic and manual.
3.1 Manually
If you want to do it manually, open Notepad on Windows or TextEdit on a Mac and write down the kind of instructions you want Codex to follow. Please note that you only need to write these instructions in plain language. You don't need to use any coding or programming language.
You can divide AGENTS.md file into following sections:
#Role
The hash sign here indicates that it's a heading.
Describe the kind of role you would like Codex to assume as your research assistant. Give it a few details about your research field and current project.
#Standards
Describe academic standards relevant to your field of research. For example, you can tell Codex to follow a given citation style or a specific structure of a research paper.
#Writing Style
Tell Codex the kind of writing style you would like it to follow, whether you want it to respond in academic style or in an informal style.
#Critique Style
Describe how you would like Codex to critique your work, whether you would like to focus on your argument, evidence, or methodology.
Save the file as AGENTS.md in your main project folder on your computer and you are done.
You don't need to have a perfectly crafted AGENTS.md file. You can always go back and edit it as your project evolves.
3.2 Automatically
If you don't want to create an AGENTS.md file manually, simply start a chat session in Codex and give it details about its role, standard, writing style, and critique style. Then ask it to create an AGENTS.md file using this information.
Codex will create the file and save it to your project folder.
3.3 Memory and Project Context
As you work through your project, Codex can use the instructions and files in your project folder as context. Some Codex setups may also have memory features, but you should not rely on hidden memory as the main way Codex remembers your project.
Each time you start a session, Codex can read AGENTS.md and the project files you ask it to inspect and uses them to answer your questions.
Over time, your instructions and visible project notes give Codex enough context for you and your work that it becomes a reliable research assistant.
You can ask Codex about its instructions by typing "Tell me what instructions you are following for this project." If a certain piece of information is outdated (e.g. a citation style), simply update AGENTS.md with the new information.
3.4 What Not to Put in AGENTS.md
Don't put any confidential information in AGENTS.md or anything that you don't want the AI to use.
Don't let AGENTS.md become a set of outdated information because that will have considerable impact on its output. You may want to update the file every few weeks.
Part 4: Working with Your Research Documents
A Codex folder does not have to be very neatly organized. This doesn't mean you start putting irrelevant files in this folder. What it means is that you should not spend any time organizing it before you begin. Codex can help you do that. The only thing you may want to keep in mind is not to give your files confusing names like Dissertation (final) (final2) (use this one).
Add a bunch of PDFs, Word files, datasets, interview transcripts, etc. related to your project.
Suppose you have twenty research papers related to your research topic and you want to find a common theme that runs across all of them. Or maybe you have a certain claim or an argument, and you are looking for papers that present evidence supporting or contrasting that claim.
Open the folder in Codex and write a prompt like:
Read every PDF in this folder and tell me which articles disagree with the following argument: [paste the argument here]
Codex will read the PDFs it can access in the folder and will give you the relevant information from these articles. Codex's answer may be in the form of a table.
4.1 Research Assistant for Literature Review
If you are a biomedical researcher or a social scientist who frequently runs systematic reviews, download fifty research articles and put them in a folder titled "Systematic Review with Codex."
Open the folder in Codex and give it your screening (inclusion/exclusion) criteria and ask it to screen all the papers in the folder.
Codex will screen the papers according to your criteria and give you the results in the form of a table. You should still verify the results yourself before relying on them.
4.2 Working with Transcripts
If you are qualitative researcher, you can add interview transcripts in the Codex folder and ask it extract information related to a given topic.
For example, you can ask it to extract how each respondent answers a given question.
4.3 Give Codex a Tedious Task
Put fifty-odd PDFs in a folder and open it in Codex. Then ask it to go through them all and rename them using their titles.
You will see that Codex has done the needful in a couple of minutes. In the beginning, ask it to show you the proposed new names before actually renaming the files.
4.4 Asking Codex to Create Files
Since your project is going to evolve, you would want Codex to create certain files for you too so that you can go back to them if needed. It will also help Codex with easy retrieval as the project develops.
Anytime you ask Codex to do a significant task like screening papers or extracting information from transcripts, ask it to save your answer in folder as a file.
Generally, Codex will save these files as markdown (md), which take up very less space and are very easy for Codex to retrieve information from. But you can also ask it to create a Word file or an Excel sheet.
Part 5: Codex Skills
A Skill is a set of instructions that makes Codex a specialist for one task. Just like AGENTS.md file, a Skill is also written in plain English, but in Codex it usually lives in a folder with a file called SKILL.md. And just like AGENTS.md, you can create a Skill file both manually and automatically.
Once you create a Skill, Codex can use it when the task matches the Skill description. You can also invoke a Skill yourself by name, for example by typing something like “$skill-name” your prompt.
The easiest way to create a Skill is to ask Codex to do it for you. Let's say, you have regular Zoom calls, and you have transcripts of those calls. For every call or transcript, you want to extract actionable items or things to do.
To create a Skill, start a Codex session and simply ask it to create a Skill for extracting actionable items from Zoom transcripts.
Codex will get to work. It may ask you follow-up questions and create a Skill file that you can edit if you want to. Maybe you want Codex to follow a specific structure while responding.
Once the Skill is created, restart Codex or reload the project and the Skill will be ready to use.
5.1 Difference between AGENTS.md and Skills
AGENTS.md contains global or project-level instructions about you and your project. It gives Codex the big picture about you and your research.
Skills, on the other hand, are meant for particular tasks. These files contain information that are much more specific and granular. AGENTS.md, Skills, and visible project notes work in concert to give you the best possible response.
5.2 What Not to Delegate to Codex
Codex is great at labor-intensive, time-consuming, and repetitive tasks. Outsource these tasks to Codex. But Codex will not be able to create what actually counts as scholarship because it won't be able to give you new and original arguments.
It can synthesize information that you can then use in service of your argument, but the job of coming up with an original argument remains yours as a researcher.
