More text + formatting

docs/demo/PREPARATIONS.md

@@ -10,7 +10,7 @@ So download the following structures should be from the PDB database:
 
 The files are available in the `./input` directory.
 
-The cli needs preprocessing, the webapp can use PDB files straight from the PDB database and will do preprocessing for you. 
+The cli needs preprocessing, the webapp can use PDB files straight from the PDB database and will do preprocessing for you.
 
 ### Step 2: Start the webapp locally
 
@@ -26,7 +26,7 @@ Goto http://localhost:8000/register and fill in the form.
 
 ### Step 4: Enable light mode and use easy expertise level
 
-1. Goto http://localhost:8000/profile 
+1. Goto http://localhost:8000/profile
 2. Select easy expertise level (this will make the job builder less busy)
 3. Select light mode.
 
@@ -45,7 +45,7 @@ Goto http://localhost:8000/register and fill in the form.
 ### Step 5b: Add completed job
 
 1. Download the `antibody-antigen-completed.zip` from SURFDrive
-2. Goto http://localhost:8000/upload 
+2. Goto http://localhost:8000/upload
 3. Select output zip option
 4. Upload the files from the `./antibody-antigen-completed.zip`.
 5. After completion check that report and browse page work

docs/demo/README.md

@@ -10,24 +10,28 @@ From the original tutorial we use scenario 2b: Docking using the paratope and th
 2. Goto scenarios page
 3. Goto Antibody-antigen scenario page
 4. For antibody
-  1. Upload `./input/4G6K.pdb` file
-  2. Select chain H
-  3. Import active residues: `31,32,33,34,35,52,54,55,56,100,101,102,103,104,105,106,1031,1032,1049,1050,1053,1091,1092,1093,1094,1096`
-5. For antigen
+5. Upload `./input/4G6K.pdb` file
+6. Select chain H
+7. Import active residues: `31,32,33,34,35,52,54,55,56,100,101,102,103,104,105,106,1031,1032,1049,1050,1053,1091,1092,1093,1094,1096`
+8. For antigen
    1. Upload `./input/4I1B.pdb`
    2. Import active residues: `72,73,74,75,81,83,84,89,90,92,94,96,97,98,115,116,117`
-6. For reference structure upload `./input/4G6M.pdb` file.
-7. Refine in builder
+9. For reference structure upload `./input/4G6M.pdb` file.
+10. Refine in builder
 
 Do not submit as this will render laptop unusable for a while.
 
 1. Goto http://localhost:8000/jobs
 2. Open job named `antibody-antigen-completed`
-3. Goto report page
+3. Goto report page,
 4. Goto browse page
 
+TODO add conclusion adapted from original tutorial here
+
 ## Features
 
+Features of the web application that are nice to show off.
+
 ### Scenario page
 
 [![Screenshot of filled antibody antigen scenario page](./screenshots/scenario_antibody-antigen.png)](./screenshots/scenario_antibody-antigen.png)
@@ -41,8 +45,8 @@ Do not submit as this will render laptop unusable for a while.
 1. Select rigibody module
 2. Expand sampling
 3. Change to text tab
-4. Change number of models to generate to 2000 
- 
+4. Change number of models to generate to 2000
+
 See how form and text visualization are synchronized.
 
 ### Report page
@@ -55,7 +59,21 @@ If you found looking at the results that you want use a slightly different workf
 
 An uploadied completed job can not be edited. So use an actual locally run job if you want to show that off.
 
-## Talking Points
+## Talking points
+
+### What is HADDOCK?
+
+Is software that tries to figure out how 2 or more molecules can fit together using information to tell which parts are important.
+
+HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes.
+
+HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. It also allows to define specific unambiguous distance restraints (e.g. from MS cross-links) and supports a variety of other experimental data including NMR residual dipolar couplings, pseudo contact shifts and cryo-EM maps.
+HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes, including multi-bodies (N>2) assemblies.
+
+### Usage of software
+
+The HADDOCK2 web application has on average 100 jobs per day and over 50.000 registered users.
+See https://rascar.science.uu.nl/stats
 
 ### HADDOCK3 vs HADDOCK2
 
@@ -70,11 +88,14 @@ An uploadied completed job can not be edited. So use an actual locally run job i
 The HADDOCK2 web application at https://rascar.science.uu.nl/haddock2.4/ only allows for docking.
 With HADDOCK3 web application you can still do docking, but also pick from several other scenarios or build a workflow from scratch.
 
+The HADDOCK3 web application can be run by anyone, while the HADDOCK2 web application is only available to the BonvinLab.
+Pharmaceutical companies can run their own HADDOCK3 web application and their data can stay on their own network.
+
 ### Re-usablity of software
 
 1. The workflow builder is a seperate piece of software that can be used in other projects to make a configuration file. You just need defined a JSON schema for the modules/nodes and use TOML format for the workflow output. See https://github.com/i-VRESSE/workflow-builder
 2. The jobs are executed by the bartender web service, which written in Python and can handle running jobs in a locally, pilot job system, slurm batch scheduler or on the grid using DIRAC. See https://i-vresse-bartender.readthedocs.io/
-3. The 
+3. Generic UI components are in own package called [haddock3-ui](https://github.com/i-VRESSE/haddock3-ui). The HADDOCK3 CLI also uses this package to render clusters.
 
 ### Implementation details