references, mermaid diagram of notebooks

paper/organising.md

@@ -27,5 +27,16 @@ The current plan for writing up the paper is as follows:
 
 ## Current known contributors
 
+```{note} On this page, not all links to sections of the paper work, [follow this link for the working version](./paper.md#contributors).
+```
+
 ```{include} sections/contributor_table.md
 ```
+
+## Notebook map
+
+```{note} On this page, not all links to sections of the paper work, [follow this link for the working version](./paper.md#notebook-map).
+```
+
+```{include} sections/notebook_map.md
+```

paper/sections/contributor_table.md

@@ -26,10 +26,10 @@ If you add a contribution, please use one of the following templates (see exampl
   - Conceived the project, wrote the paper, wrote and recorded the Cosyne tutorial. Conducted research ([](../research/3-Starting-Notebook.ipynb)).
 * - Francesco De Santis
   - [\@francescodesantis](https://github.com/francescodesantis)
-  - Research and writing on a more detailed model ([](./sections/new_inh_model.md)).   
+  - Conducted research (TODO INCLUDE LINK), wrote the paper ([](#inh-model))
 * - Karim Habashy 
   - [\@KarimHabashy](https://github.com/KarimHabashy)
-  - Research and writing on learning delays ([](../research/Learning_delays.ipynb), [](../research/Learning_delays_major_edit2.ipynb), [](./sections/delays/Delays.md)) and help with project management ([](../research/4-Quick_Start.ipynb)).  
+  - Conducted research ([](../research/Learning_delays.ipynb), [](../research/Learning_delays_major_edit2.ipynb), [](../research/Solving_problem_with_delay_learning.ipynb)), wrote the paper ([](#delay-section)), project management ([](../research/4-Quick_Start.ipynb))
 * - Mingxuan Hong
   - [\@mxhong](https://github.com/mxhong)
   - Conducted research ([](../research/Altering_output_neurons.ipynb), [](../research/Dynamic_threshold.ipynb)).
@@ -71,7 +71,7 @@ If you add a contribution, please use one of the following templates (see exampl
   - (TODO)
 * - [Alberto Antonietti](https://www.deib.polimi.it/eng/people/details/669646)
   - [\@alberto-antonietti](https://github.com/alberto-antonietti)
-  - Supervised Francesco De Santis and wrote ([](./sections/new_inh_model.md)).
+  - Supervised Francesco De Santis, wrote the paper ([](#inh-model)).
 * - Lavínia Takarabe
   - [\@laviniamitiko](https://github.com/laviniamitiko)
   - (TODO)

paper/sections/delays/Delays.md

@@ -1,3 +1,4 @@
+(delay-section)=
 ## Learning Delays
 
 This section introduces a simple method to solve the sound localization problem with only learnable delays

paper/sections/new_inh_model.md

@@ -1,3 +1,4 @@
+(inh-model)=
 ## Contralateral glycinergic inhibition as key factor in creating ITD sensitivity
 
 ### Intro

paper/sections/notebook_map.md

@@ -1,5 +1,25 @@
 The following lists the notebooks, authors, summary and related notebooks in this project.
 
+% this will only appear on the online version, not in the printed version
+```{mermaid}
+flowchart LR
+    SN[Starting Notebook] --> QS[Quick Start Notebook]
+    Dale --> QS
+    Tau --> QS
+    SN --> FF[Filter-and-Fire Neuron Model]
+    SN --> AON[Altering Output Neurons]
+    ATN --> AW[Analysing trained networks - workshop edition]
+    SN --> Dale[Sound localisation following Dale's law]
+    SN --> DThr[Dynamic threshold]
+    SN --> Exc[Sound localisation using excitatory-only inputs]
+    SN --> DDL[Learning delays]
+    SN --> DCLS[Dilated Convolution with Learnable Spacings]
+    SN --> Rob[Robustness to Noise and Dropout]
+    SN --> V250[Version with 250 Hz Input]
+    SN --> ATN[Analysing trained networks]
+    SN --> Tau[Optimizing the membrane time constant]
+```
+
 ## Introductory notebooks
 
 [](../research/1-Background.md)
@@ -25,7 +45,7 @@ The following lists the notebooks, authors, summary and related notebooks in thi
     : Comparison of three different ways of reading out the network's decision (average membrane potential, maximum membrane potential, spiking outputs) with short and long time constants. (Author: Mingxuan Hong.)
 
 [](../research/Analysing-Trained-Networks-Part2.ipynb)
-    : Group project from an early workshop looking at hidden unit spiking activity and single unit ablations. Found that some hidden neurons don't spike, and ablating those does not harm performance. Builds on [](../research/Analysing-Trained-Networks.ipynb). (Author: Gabriel Béna, Josh Bourne, Tomas Fiers, Tanushri Kabra, Zekai Xu. TODO SURNAMES.)
+    : Group project from an early workshop looking at hidden unit spiking activity and single unit ablations. Found that some hidden neurons don't spike, and ablating those does not harm performance. Builds on [](../research/Analysing-Trained-Networks.ipynb). (Author: Gabriel Béna, Josh Bourne, Tomas Fiers, Tanushri Kabra, Zekai Xu.)
 
 [](../research/Dales_law.ipynb)
     : Investigation into the results of imposing Dale's law. Incorporated into [](../research/4-Quick_Start.ipynb). Uses a fix from [](../research/IE-neuron-distribution.ipynb). (Author: Marcus Ghosh, Gabriel Béna, Jose Gomes.)