Reorganize documentation files and update setup instructions

.devcontainer/postStartCommand.sh

@@ -63,6 +63,12 @@ cat > /workspaces/docs/README.ipynb << EOL
 }
 EOL
 
+# Create an empty .env file if it doesn't exist
+if [ ! -f /workspaces/docs/.env ]; then
+  echo "# Auto-generated .env file" > /workspaces/docs/.env
+  echo "Creating empty .env file because none was found."
+fi
+
 # Display welcome message
 echo ""
 echo "🧪 LAB AGENT ENVIRONMENT READY 🧪"

ENVIRONMENT_SETUP.md

@@ -47,6 +47,23 @@ export OPENAI_API_KEY="your-openai-api-key"
 3. Add `.env` to your `.gitignore` to prevent accidentally committing your API key
 4. Rebuild your container
 
+## Environment Variables
+
+### Setting up .env file
+
+The development environment requires a `.env` file in the root directory of the repository. This file is not included in Git (it's gitignored) because it may contain sensitive information.
+
+**Before starting a codespace:**
+
+1. Create a `.env` file in the root directory
+2. The file can be empty if you don't need any environment variables
+3. If you need to use OpenAI API features, add your key like this:
+   ```
+   OPENAI_API_KEY=your_api_key_here
+   ```
+
+**Note:** Without a `.env` file (even an empty one), the codespace environment will fail to start.
+
 ## Verifying Your Setup
 
 After completing these steps, you can verify your setup by running:

README.md

@@ -7,6 +7,7 @@
 Welcome to the Lab Codespace! This environment is pre-configured for you. Just follow these steps:
 
 ## 🚀 1. Open the Codespace
+
 - Click "Code" > "Codespaces" > "Create codespace on main" (or your assigned branch).
 
 ## ⏳ 2. Wait for Setup

aims.md

@@ -0,0 +1,48 @@
+1. Ybx1 in adipogenesis
+   1. Identifying YBX1-CEBPA-cBAF interactions in early, middle, late 3T3-L1 adipogenesis LO
+      1. Are we seeing this in all cell types?
+   2. YBX1 in adipogenic 3T3 metabolism ?
+   3. Loss of SMARCD2, SMARCE1, and YBX1 in differentating 3T3 cells CJ
+2. cBAF-CEBPa regulating mir-101 ?
+3. Ybx1 in metabolic reprogramming of hepatocytes
+   1. PPARg, CEBPa, CEBPb, SMARCD2, SMARCE1, BRG1
+   2. Posttranscriptional regulation of lipogenic genes by Ybx1
+   3. YBX1 INS1 repression
+      1. All cells except pancreatic beta cells?
+         1. Absent in pancreatic beta cells?
+            1. If so, how?
+         2. Targeting YBX1 in certain types of Type 1 diabetes mellitus
+   4. YBX1-CEBPa-cBAF in lipid-exposed hepatocytes multiomics
+      1. mRNAseq
+      2. ATACseq
+      3. ChIPseq:
+         1. YBX1,
+         2. BRG1,
+         3. CEBPa,
+         4. (and CEBPb).
+4. Using artificial intelligence to enhance biological insights
+   1. Geo stacking app ER
+   2. Transregulator-ATAC pattern finder ?
+   3. Increase read mapping speed ?
+   4. Lab agent JJ
+5. Regulation of Ybx1 cyto-nuclear translocation
+6. Metabolic regulation of gene expression
+   1. Different nutrient scenarios
+   2. Insulin, inhibit beta-oxidation, inhibit glycolysis, ATACseq
+7. Environmental affects on hepatocyte cell fate
+   1. KLFs
+   2. HepaRG
+8. Mice
+9.  Miscellaneous
+   1.  Spheroids/Organoids
+   2.  Robot
+   3.  Directional RNAseq
+   4.  DuoLink
+   5.  FA Uptake
+   6.  Proliferation
+   7.  Lipidomics
+   8.  Oxylipins
+   9.  CelSeq time series
+   10. In vitro cytonuclear proteomics
+       1.  Epigenetic memory
+           1.  Mismatch