29 | `,
30 | },
31 | }),
32 | instantsearch.widgets.pagination({
33 | container: '#pagination',
34 | }),
35 | ]);
36 |
37 | search.start();
38 |
--------------------------------------------------------------------------------
/exampleSite/archetypes/notes.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "{{ replace .Name "-" " " | title }}"
3 | categories:
4 | - ""
5 | tags:
6 | - ""
7 | summary: ""
8 | authors:
9 | - Author A
10 | references:
11 | - name: References 1
12 | link: https://google.com
13 | date: {{ .Date }}
14 | type: project
15 | draft: false
16 | ---
--------------------------------------------------------------------------------
/exampleSite/archetypes/project.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "{{ replace .Name "-" " " | title }}"
3 | images: # not required
4 | - path: /img/projects/default.svg # not required
5 | categories:
6 | -
7 | tags:
8 | -
9 | links:
10 | -
11 | summary: ""
12 | fields:
13 | members: # the makers of the tool
14 | - name:
15 | link:
16 | description:
17 | coordinators:
18 | - name:
19 | link:
20 | description:
21 | status: Done # In Progress
22 | notes: # Link to notes
23 | - name:
24 | link:
25 | date: {{ .Date }}
26 | draft: false
27 | ---
--------------------------------------------------------------------------------
/exampleSite/content/about.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: ABOUT
3 | layout: page
4 | excerpt: ''
5 | date: 2016-03-24
6 | image:
7 | feature:
8 | credit:
9 | creditlink:
10 | ---
11 |
12 | We host reading clubs and seminars on neuroscience, machine learning, complex networks and intelligence.
13 |
14 |
15 |
16 | ## License & Source
17 |
18 | Articles on this website are published under CC BY-NC-SA license if no specific license is designated.
19 |
20 |
21 | 
22 |
23 |
24 | * This website is hosted on [GitHub](https://github.com/neuronstar/neuronstar.github.io) and generated by GitHub Pages (hugo).
25 | * [Computational Neuroscience Map](http://neuronstar.cc/comp-neurosci-map/) is written in [TiddlyMap](tiddlymap.org) and hosted statically on GitHub Pages.
26 |
--------------------------------------------------------------------------------
/exampleSite/content/esl/_index.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "The Element of Statistical Learning"
3 | description: "This is a set of notes"
4 | type: project
5 | ---
--------------------------------------------------------------------------------
/exampleSite/content/esl/assets/00.The-Elements-of-Statistical-Learning/10dsphere-volume-vs-radius.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/esl/assets/00.The-Elements-of-Statistical-Learning/10dsphere-volume-vs-radius.png
--------------------------------------------------------------------------------
/exampleSite/content/esl/assets/04.shrinkage-methods/shrinkage-lq-norm.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/esl/assets/04.shrinkage-methods/shrinkage-lq-norm.png
--------------------------------------------------------------------------------
/exampleSite/content/esl/assets/misc/timezones-1.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/esl/assets/misc/timezones-1.jpg
--------------------------------------------------------------------------------
/exampleSite/content/esl/assets/misc/timezones-2.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/esl/assets/misc/timezones-2.jpg
--------------------------------------------------------------------------------
/exampleSite/content/esl/gauss-markov-theorem.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Guass-Markov Theorem and Multiple Regression"
3 | date: 2016-09-01
4 | authors:
5 | - OctoMiao
6 | summary: Gauss-Markov Theorem
7 | type: project
8 | tags:
9 | - Statistics
10 | - "Gauss-Markov Theorem"
11 | links:
12 | - snm/limitations-srm-contd-and-coding.md
13 | - snm/single-neuron-model.md
14 | weight: 3
15 | ---
16 |
17 |
18 | ## Gauss-Markov
19 |
20 | 1. "**Least squares** estimates the parameters $\beta$ have the smallest variance among all linear unbiased estimates."
21 | 2. **Unbiased estimation** is not always good.
22 | 3. ridge regression
23 |
24 | ### Proof of 1
25 |
26 | 1. Model: $\theta = a^T \beta$
27 | 2. Least square estimate of $\theta$: $\hat\theta = a^T \hat \beta = a^T ( \mathbf X^T \mathbf X )^{-1} \mathbf X^T \mathbf y = \mathbf c_0^T \mathbf y$
28 | 3. This is unbiased: $E(a^T\hat\beta) = a^T\beta$
29 | 4. Gauss-Markov theorem: If we have any other linear estimator $\tilde \theta = \mathbf c^T \mathbf y$ and $E(\mathbf c^T \mathbf y)=a^T \beta$, then $Var(a^T\hat \beta)\leq Var(\mathbf c^T \mathbf y)$.
30 | 5. To prove it we first write down the general form of a linear estimator. **Question:** is the general form of a linear estimator $\alpha (X^T X)^{-1} X^T + D$?
31 |
32 |
33 |
34 | Useful functions for the proof:
35 |
36 | 1. Variance: $Var(X) = E[ (X - \mu)^2 ]$.
37 | 2. [On wikipedia](https://en.wikipedia.org/wiki/Gauss%E2%80%93Markov_theorem#Proof)
38 |
39 |
40 | 1. MSE: $MSE(\tilde\theta) = E( (\tilde\theta -\theta)^2 ) = E( (\tilde \theta - E(\theta) + E(\theta) - \theta)^2 ) = E( (\tilde\theta - E(\theta))^2 ) + \cdots$
41 | 2. MSE is $MSE(\tilde \theta) = Var(\tilde theta) + (E(\theta) -\theta)^2$ the second term is bias.
42 | 3. Least square is good but we can trade some bias to get a smaller variance sometimes.
43 | 4. Choices are variable subset selection, ridge regression.
44 |
45 |
46 |
47 | 1. Suppose new data is biased from the original data by a value $\epsilon_0$, the MSE using the original estimator is only the original MSE differed by a constant. Eq. 3.22
48 | 2. We always have a larger MSE????? I don't get this.
49 |
50 |
51 | ## Multiple Regression
52 |
53 | 1. Model: $f(X) = \beta_0 + \sum_{j=1}^p X_j \beta$
54 | 2. For multiple dimensional inputs, the estimator has no correlations for different features.
55 |
--------------------------------------------------------------------------------
/exampleSite/content/esl/linear-methods-for-regresssion.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Linear Methods for Regression"
3 | date: 2016-08-18
4 | authors:
5 | - OctoMiao
6 | summary: Linear regression, least squares
7 | type: project
8 | weight: 2
9 | ---
10 |
11 |
12 | ## Some Interesting Points
13 |
14 |
15 | 1. Geometrically speaking, linear regression methods finds the closest path from the true data to a hypersurface spanned by the data vectors. By definition, each set of data is viewed as a basis vector. The so called closed path to the hypersurface is basically the path that is perpendicular to the surface. Thus we know the prediction we are looking for is a projection of true data onto the hypersurface.
16 | 2. The argument above also indicates that degenerate data set, which contains data of the same direction, could cause problems since we have a redundant basis.
17 | 3. Distribution of the parameters can be obtained for some categories of data. It might be a normal distribution.
18 | 4. t-distribution, aka [student's t-distribution](https://en.wikipedia.org/wiki/Student%27s_t-distribution), is a category of distributions describing the deviation of estimated mean in a normal distribution from the true mean.
19 | 5. The tail of the estimated distribution approaches the actual tail distribution as the sample size increases.
20 | 6. Z score can be used to test the significance of the statistics.
21 | > "Roughly a Z score larger than two in absolute value is significantly nonzero at the p=0.05 level."
22 | > The author said in the caption of Table 3.2
23 | 7. [F statistic](https://en.wikipedia.org/wiki/F-statistic)
24 |
25 |
26 | Confusion:
27 |
28 | 1. Eqn 3.14: plug in the definition of z and read again.
29 |
--------------------------------------------------------------------------------
/exampleSite/content/graph/_index.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: Graph of the whole knowledge base
3 | ---
--------------------------------------------------------------------------------
/exampleSite/content/posts/_index.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Blog Posts"
3 | ---
--------------------------------------------------------------------------------
/exampleSite/content/projects/assets/tutorials/backlink-box.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/projects/assets/tutorials/backlink-box.png
--------------------------------------------------------------------------------
/exampleSite/content/projects/assets/tutorials/backlink-notes.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/projects/assets/tutorials/backlink-notes.jpg
--------------------------------------------------------------------------------
/exampleSite/content/projects/assets/tutorials/graph-of-notes.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/projects/assets/tutorials/graph-of-notes.jpg
--------------------------------------------------------------------------------
/exampleSite/content/projects/snm.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Spiking Neuron Models"
3 | categories:
4 | - Neuroscience
5 | tags:
6 | - Introduction
7 | - Neuroscience
8 | links:
9 | -
10 | summary: Reading club for the book Spiking Neuron Models
11 | images:
12 | - "/projects/undraw_design_thinking_re_644h.svg"
13 | members: # the makers of the tool
14 | - name: Member AA
15 | link: https://google.com
16 | description:
17 | coordinators:
18 | - name: LM
19 | link:
20 | description:
21 | date: 2020-04-27T13:22:46+02:00
22 | status: Done
23 | sections:
24 | - snm
25 | references:
26 | - name: "Spiking Neuron Models: Single Neurons, Populations,Plasticity by Wulfram Gerstner and Werner M. Kistler."
27 | link: http://lcn.epfl.ch/~gerstner/SPNM/SPNM.html
28 | - name: "An Introduction to the Theory of Point Processes by D.J. Daley and D. Vere-Jones."
29 | link: https://github.com/neuronstar/spiking-neuron-models/issues/12
30 | ---
31 |
32 | ## What books are we reading?
33 |
34 | 1. [Spiking Neuron Models: Single Neurons, Populations,Plasticity](http://lcn.epfl.ch/~gerstner/SPNM/SPNM.html) by Wulfram Gerstner and Werner M. Kistler.
35 | 2. [An Introduction to the Theory of Point Processes](https://github.com/neuronstar/spiking-neuron-models/issues/12) by D.J. Daley and D. Vere-Jones.
36 |
37 | ## When and How
38 |
39 | The discussion is online through Skype. It is usually held during the weekends.
40 |
41 | ## More
42 |
43 | Please watch the GitHub repo: [neuronstar/spiking-neuron-models](https://github.com/neuronstar/spiking-neuron-models)
44 |
--------------------------------------------------------------------------------
/exampleSite/content/projects/tutorials.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Connectome Tutorials"
3 | images:
4 | - "/projects/undraw_video_influencer_-9-oyy.svg"
5 | categories:
6 | - Tutorials
7 | tags:
8 | - Introduction
9 | - Tutorials
10 | members: # the makers of the tool
11 | - name: KausalFlow
12 | link: https://kausalflow.com
13 | description:
14 | coordinators:
15 | - name: KausalFlow
16 | link: https://kausalflow.com
17 | description:
18 | date: 2021-04-27T13:22:46+02:00
19 | status: Done
20 | sections:
21 | - tutorials
22 | ---
23 |
24 | This is a set of tutorials on how to use the connectome Hugo theme.
25 |
26 |
27 | The connectome Hugo theme is focusing on connecting notes with backlinks. Suppose a note A is linking to note B, note B should know that note A is linking to itself. In this setup, we immediately realize that we probably want to read about note A when viewing note B.
28 |
29 |
30 | {{< figure src="../assets/tutorials/backlink-notes.jpg" >}}
31 |
32 |
33 | The following is an example of such backlinks in this note {{< c "tutorials/embed-articles.md" >}}
34 |
35 | {{< figure src="../assets/tutorials/backlink-box.png" >}}
36 |
37 |
38 | What is more, the connectome Hugo theme also provides a {{< c "graph" "graph view of all the notes" >}}.
39 |
40 | {{< figure src="../assets/tutorials/graph-of-notes.jpg" >}}
41 |
42 | In this tutorial, we will demonstrate how to achieve this using the connectome Hugo theme.
--------------------------------------------------------------------------------
/exampleSite/content/snm/_index.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Spiking Neural Network"
3 | type: project
4 | ---
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/adaptation-of-neurons.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/adaptation-of-neurons.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/population-vector-coding.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/population-vector-coding.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/reversed-ipsp.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/reversed-ipsp.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/saturation.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/saturation.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/simple-spike-coding-model-of-visual.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/simple-spike-coding-model-of-visual.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/synchronized-for-same-objects.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/limitations-srm-contd-and-coding/synchronized-for-same-objects.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/synchronized-oscillations-and-locking/step-like-population-activity.ggb:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/synchronized-oscillations-and-locking/step-like-population-activity.ggb
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/synchronized-oscillations-and-locking/step-like-population-activity.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/synchronized-oscillations-and-locking/step-like-population-activity.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/tf_synchro_bursting/raster_bursting.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/tf_synchro_bursting/raster_bursting.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/tf_synchro_bursting/time_evol_bursting.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/tf_synchro_bursting/time_evol_bursting.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/assets/tf_synchro_bursting/trajectory_ps.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/snm/assets/tf_synchro_bursting/trajectory_ps.png
--------------------------------------------------------------------------------
/exampleSite/content/snm/single-neuron-model.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: notes
3 | title: "Single Neuron Models"
4 | date: 2016-03-18
5 | authors:
6 | - ErbB4
7 | summary: Neuron biological properties
8 | type: project
9 | links:
10 | - snm/limitations-srm-contd-and-coding.md
11 | - snm/single-neuron-model.md
12 | weight: 2
13 | ---
14 |
15 |
16 | ## Neuron biological properties
17 |
18 | Dendrites receive neurotransmitter and generate local post-synaptic potential (PSP), either excitatory by glutamate or inhibitory by GABA. Soma integrates all PSPs. Once membrane potential reaches the threshold, an action potential is generated. Action potentials are propagated via axon.
19 |
20 | ### Spike Response Model (SRM)
21 |
22 | In this model, membrane potential is denoted as u(t). When the neuron is at rest state, receiving no external stimulation, the membrane potential is called rest potential.
23 |
24 |
25 | $$u(t_0)=u_{\mathrm{rest}}.$$
26 |
27 |
28 | When a presynaptic spike arrives, there is a local PSP, causing a small disturbance in membrane potential.
29 |
30 | $$u(t)-u_{\mathrm{rest}} = e_{ij}.$$
31 |
32 | Throughout the notes, $i$ is always indicating the neuron we are measuring the potential, while $j$ is for the incoming signal.
33 |
34 | According to simplification rule, all PSPs are integrated linearly.
35 |
36 | $$u_i(t) =u_{\mathrm{rest}}+ \sum_{j} \sum_f \epsilon_{ij}(t - t_j^{(f)}) $$
37 |
38 | in which $(f)$ shows the $j$ neurons can fire multiple times.
39 |
40 | However, when an action potential is generated, there is a dramatic membrane potential change (depolarization), and due to the electrophysiological property of channels, hyperpolarization phenomenon is observed. So the complete but simple presentation of membrane potential is
41 |
42 | $$u_i(t) =u_{\mathrm{rest}}+ \sum_{j} \sum_f \epsilon_{ij}(t - t_j^{(f)}) + \eta(t-\hat t_i),$$
43 |
44 | where $\hat t_i$ is the moment when the action potential is triggered.
45 |
46 |
47 |
48 | ### Spike train
49 |
50 | When simulating a neural network, we don't care about the exact trajectory of membrane potential.
51 | so Dirac function is used to present an action potential. This provides the first step to computation, using firing times to present the spike train of a neuron.
52 |
53 | ### Limitation of SRM
54 |
55 | SRM cares about merely the most recent spike, however in real case, previous spikes could influence the reaction of the neuron to a later simulation. (for example, by changing membrane conductivity)
56 |
--------------------------------------------------------------------------------
/exampleSite/content/snm/spiking-neuron-models-club.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: notes
3 | title: "Spiking Neuron Models Reading Club"
4 | date: 2016-03-18
5 | authors:
6 | - ErbB4
7 | summary: Introduction to reading club of spiking neuron models, schedule, and notice
8 | type: project
9 | links:
10 | - snm/limitations-srm-contd-and-coding.md
11 | - snm/single-neuron-model.md
12 | weight: 1
13 | ---
14 |
15 |
16 | ## What books are we reading?
17 |
18 | 1. [Spiking Neuron Models: Single Neurons, Populations,Plasticity](http://lcn.epfl.ch/~gerstner/SPNM/SPNM.html) by Wulfram Gerstner and Werner M. Kistler.
19 | 2. [An Introduction to the Theory of Point Processes](https://github.com/neuronstar/spiking-neuron-models/issues/12) by D.J. Daley and D. Vere-Jones.
20 |
21 | ## When and How
22 |
23 | The discussion is online through Skype. It is usually held during the weekends.
24 |
25 | ## More
26 |
27 | Please watch the GitHub repo: [neuronstar/spiking-neuron-models](https://github.com/neuronstar/spiking-neuron-models)
28 |
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/_index.md:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Tutorials"
3 | description: "Tutorial articles for Hugo Connectome Theme"
4 | type: project
5 | ---
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/command-palette/command-palette-demo.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/command-palette/command-palette-demo.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/command-palette/command-palette-note-commands-demo-less.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/command-palette/command-palette-note-commands-demo-less.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/command-palette/command-palette-note-commands-demo.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/command-palette/command-palette-note-commands-demo.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/graph-of-connected-articles/graph-alpha.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/graph-of-connected-articles/graph-alpha.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/graph-of-connected-articles/graph-page.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/graph-of-connected-articles/graph-page.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/graph-of-connected-articles/graph.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/graph-of-connected-articles/graph.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/link-articles/current-ref.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/link-articles/current-ref.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/nav-buttons-at-bottom/lyket.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/nav-buttons-at-bottom/lyket.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/tutorials/backlink-box.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/tutorials/backlink-box.png
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/tutorials/backlink-notes.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/tutorials/backlink-notes.jpg
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/assets/tutorials/graph-of-notes.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/kausalflow/connectome/472c5d5133ff7789e3fd0675437eef6bdd40d226/exampleSite/content/tutorials/assets/tutorials/graph-of-notes.jpg
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/command-palette.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Command Palette"
4 | date: 2021-05-01
5 | tags:
6 | - Tutorial
7 | authors:
8 | - KausalFlow
9 | links:
10 | - tutorials/_index.md
11 | weight: 8
12 | ---
13 |
14 | To use the command palette, press Command + k (on Mac) or Windows + k (on Windows).
15 |
16 | {{< figure src="../assets/command-palette/command-palette-demo.png" >}}
17 |
18 | There are some generic commands we can use on every page, e.g.,
19 |
20 | - `Home`: navigate back to home page,
21 | - `View Graph`: navigate to the graph page,
22 | - `All Notebooks`: navigate to the notebook list,
23 | - `Search`: search notes by title, which is less powerful than the search bar on the home page.
24 |
25 | On note pages, we can use note specific commands, e.g.,
26 |
27 | - `Current Note ID`: copy the current note id to the clipboard,
28 | - `Backlinks`: show backlinks and go to backlinks,
29 | - `Links`: show all the notes that the current note linked to,
30 | - `References`: list all the references and go to the links if there is a url.
31 |
32 | {{< figure src="../assets/command-palette/command-palette-note-commands-demo.png" caption="Depending on the note, not every command is available." >}}
33 |
34 | The command palette is enabled by default. If one would like to disable it,
35 |
36 | ```yaml
37 | params:
38 | # some other configs
39 | # ...
40 | command: false
41 | ```
42 |
43 |
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/comment-system.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Comments"
4 | date: 2021-05-01
5 | tags:
6 | - Tutorial
7 | authors:
8 | - KausalFlow
9 | links:
10 | - tutorials/_index.md
11 | weight: 2
12 | ---
13 |
14 | Hugo connectome supports two comment systems:
15 |
16 | - utteranc.es, and
17 | - giscus.
18 |
19 | {{< message class="warning" title="Optional" >}}
20 | This step is optional. It is up to the user to decide whether to configure a comment system or not.
21 | {{< /message >}}
22 |
23 | Here is a demo config. We put both giscus and utterances here but we only `use: "giscus"`.
24 |
25 |
26 | ```yaml
27 | comments:
28 | use: "giscus"
29 | giscus:
30 | repo: "datumorphism/comments"
31 | repo_id: "MDEwOlJlcG9zaXRvcnkxNjU5MDkyNDI="
32 | category: "Comments"
33 | category_id: "DIC_kwDOCeOS-s4B-Zxx"
34 | utterances: # comment system: utterances (https://utteranc.es/) parameters
35 | repo: "datumorphism/comments" # repo="[ENTER REPO HERE]", the comments will appear as issues in this repository on github.
36 | term: pathname # issue-term="pathname"
37 | theme: github-light # theme="github-light"
38 | ```
39 |
40 | ## utteranc.es
41 |
42 | The comment box is using [utteranc.es](https://utteranc.es/). This is a demo configuration in the `config.yaml` file.
43 |
44 | ```yaml
45 | comments:
46 | use: "utterances"
47 | utterances: # comment system: utterances (https://utteranc.es/) parameters
48 | repo: "kausalflow/hugo-connectome-theme-demo" # repo="[ENTER REPO HERE]", the comments will appear as issues in this repository on github.
49 | term: pathname # issue-term="pathname"
50 | theme: github-light # theme="github-light"
51 | ```
52 |
53 | ## giscus
54 |
55 | See official docs: [giscus.app](https://giscus.app/)
56 |
57 | ```yaml
58 | comments:
59 | use: "giscus"
60 | giscus:
61 | repo: "kausalflow/hugo-connectome-theme-demo"
62 | repo_id: "just put your id here"
63 | category: "Your category"
64 | category_id: "bla bla bla"
65 | ```
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/embed-articles.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Embed Articles"
4 | summary: "Embed an article using the shortcode"
5 | date: 2021-05-08
6 | authors:
7 | - KausalFlow
8 | tags:
9 | - Tutorial
10 | links:
11 | - tutorials/_index.md
12 | - tutorials/link-articles.md
13 | - tutorials/graph-of-connected-articles.md
14 | weight: 6
15 | ---
16 |
17 | Embed an article using the shortcode
18 |
19 |
20 | ```go
21 | {{}}
22 | ```
23 |
24 | Here is the result:
25 |
26 |
27 | {{< e "tutorials/graph-of-connected-articles.md" >}}
28 |
29 | The shortcode can take two arguments:
30 |
31 |
32 | ```go
33 | {{}}
34 | ```
35 |
36 |
37 | {{< e "tutorials/graph-of-connected-articles.md" "This is a custom title" >}}
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/graph-of-connected-articles.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Graph of Connected Articles"
4 | date: 2021-05-01
5 | tags:
6 | - Tutorial
7 | authors:
8 | - KausalFlow
9 | links:
10 | - tutorials/link-articles.md
11 | - tutorials/_index.md
12 | weight: 1
13 | ---
14 |
15 | All articles that are connected by {{< c "tutorials/link-articles.md" "using links in metadata">}} will show up in the graph. Articles that are not connected will be hidden.
16 |
17 | {{< figure src="../assets/graph-of-connected-articles/graph-page.png" >}}
18 |
19 |
20 | We can move the canvas or drag the notes. Hover on one of the nodes to highlight the connections and see some details about the note.
21 |
22 | {{< figure src="../assets/graph-of-connected-articles/graph.png" >}}
23 |
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/how-to-use.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "How to Use"
4 | date: 2021-05-01
5 | tags:
6 | - Tutorial
7 | authors:
8 | - KausalFlow
9 | links:
10 | - tutorials/_index.md
11 | weight: 0
12 | ---
13 |
14 | - Load the themes in a folder inside `themes`. Read the [docs by Hugo](https://gohugo.io/getting-started/quick-start/#step-3-add-a-theme) for more details.
15 | - Use the `config.yaml` file in the `exampleSite` folder.
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/link-articles.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Link Articles"
4 | date: 2021-05-01
5 | tags:
6 | - Tutorial
7 | authors:
8 | - KausalFlow
9 | links:
10 | - tutorials/_index.md
11 | weight: 4
12 | ---
13 |
14 | There are three different ways to link notes:
15 |
16 | - use `links` in the note metadata, this will be covered in the current note,
17 | - use shortcode `c` to add a hyperlink in the texts, see {{< c "tutorials/link-to-other-page.md" >}},
18 | - use shortcode `e` to embed another note in the current note, see {{< c "tutorials/embed-articles.md" >}}.
19 |
20 | All three methods will generate backlinks for the notes linked to.
21 |
22 | Articles can be linked by adding a the reference of the target post to the meta data of the current post, e.g.,
23 |
24 | ```yaml
25 | links:
26 | - snm/single-neuron-model.md
27 | - tags/gauss-markov-theorem
28 | ```
29 |
30 | The ref of the target post can be
31 |
32 | - the path to the markdown file inside the `content` folder, such as `snm/single-neuron-model.md`,
33 | - the path to the tag page, such as `tags/gauss-markov-theorem`.
34 |
35 | If one needs to find the ref of a post, it is found on the right of the content. For example, the following screenshot shows the ref of this article.
36 |
37 | {{< figure src="../assets/link-articles/current-ref.png" title="Current Ref" caption="Current ref of the post is shown on the right of the articles." >}}
38 |
39 |
40 |
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/link-to-other-page.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Link to Another Page and Show Hovercard"
4 | date: 2021-05-08
5 | authors:
6 | - KausalFlow
7 | tags:
8 | - Tutorial
9 | links:
10 | - tutorials/_index.md
11 | weight: 5
12 | ---
13 |
14 | Apart from the normal markdown links, e.g.,
15 |
16 | ```markdown
17 | [this link](snm/single-neuron-model)
18 | ```
19 |
20 | we can also link to other page using the following code.
21 |
22 | ```go
23 | {{}}
24 | ```
25 |
26 | The result will be this: {{< c "tutorials/embed-articles.md" >}}. By hovering on this link, a preview of the summary of the target post.
27 |
28 |
29 | {{< message class="danger" title="Do not Ignore the Spaces" >}}
30 |
31 | Please make sure the is at least one space between the different components of the shortcode. The following shortcode will show the link just fine but will fail in creating backlinks.
32 |
33 | ```go
34 | {{}}
35 | ```
36 |
37 | {{< /message >}}
38 |
39 | ## Specify Title
40 |
41 | One can also specify a custom title for the link text.
42 |
43 | ```go
44 | {{}}
45 | ```
46 |
47 |
48 | Demo: {{< c "tutorials/embed-articles.md" "Blabla Title" >}}
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/references.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Adding References"
4 | date: 2021-05-08
5 | authors:
6 | - KausalFlow
7 | tags:
8 | - Tutorial
9 | links:
10 | - tutorials/_index.md
11 | references:
12 | - name: "Hugo (This is a demo reference)"
13 | link: "https://gohugo.com"
14 | key: "hugo"
15 | weight: 7
16 | ---
17 |
18 | One could also add references to the post. Just add the following to the meta data of the post.
19 |
20 | ```yaml
21 | references:
22 | - name: "Hugo (This is a demo reference)"
23 | link: "https://gohugo.com"
24 | ```
25 |
26 | The result is shown on the right.
27 |
28 |
29 | Inline citation of a reference is also possible if we give the reference a key.
30 |
31 | ```yaml
32 | references:
33 | - name: "Hugo (This is a demo reference)"
34 | link: "https://gohugo.com"
35 | key: "hugo"
36 | ```
37 |
38 | And in text, do the following
39 |
40 | ```go
41 | This is some description of hugo[^hugo].
42 |
43 | [^hugo]: {{}}
44 | ```
45 |
46 | The following paragraph is the rendered result of the above text.
47 |
48 | This is some description of hugo[^hugo].
49 |
50 | [^hugo]: {{< cite key="hugo" >}}
--------------------------------------------------------------------------------
/exampleSite/content/tutorials/upvote-button-at-bottom.md:
--------------------------------------------------------------------------------
1 | ---
2 | type: project
3 | title: "Upvote Button at the Bottom of the Page"
4 | date: 2021-05-01
5 | tags:
6 | - Tutorial
7 | authors:
8 | - KausalFlow
9 | links:
10 | - tutorials/_index.md
11 | weight: 3
12 | ---
13 |
14 | The small upvote and downvote nav buttons at the bottom right of the page are make with [lyket](https://lyket.dev).
15 |
16 | {{< message class="warning" title="Optional" >}}
17 | This step is optional. It is up to the user to decide whether to configure a upvote or not.
18 | {{< /message >}}
19 |
20 | This is a demo configuration.
21 |
22 | ```yaml
23 | lyket:
24 | api_key: "xxbadsjflkdjwe"
25 | lyket_type: "updown"
26 | ```
27 |
28 | To get the api token, sign up and copy the API token.
29 |
30 | {{< figure src="../assets/nav-buttons-at-bottom/lyket.png" >}}
--------------------------------------------------------------------------------
/exampleSite/content/typography.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | excerpt: Typography
4 | search_omit: false
5 | ---
6 |
7 |
8 | * ToC
9 | {:toc}
10 |
11 | ## We use kramdown
12 |
13 | This website uses [`kramdown`](http://kramdown.gettalong.org) as the basic syntax. However, a lot of html/css/js has been applied to generate some certain contents or styles.
14 |
15 | Math also follows the [`kramdown` syntax](http://kramdown.gettalong.org/syntax.html#math-blocks).
16 |
17 | ## Footnote
18 |
19 | [Syntax for footnotes is elaborated more on the website of kramdown.](http://kramdown.gettalong.org/syntax.html#footnotes)
20 |
21 | {% highlight text %}
22 | Some text here some other text here.[^1]
23 |
24 | [^1]: Footnote here
25 | {% endhighlight %}
26 |
27 |
28 | ## Table of Contents
29 |
30 |
31 | {% highlight text %}
32 | * ToC
33 | {:toc}
34 | {% endhighlight %}
35 |
36 | is used to generate table of contents.
37 |
38 | ## Figure with Caption
39 |
40 | {% highlight html %}
41 |
42 | 
43 |
44 | Caption here. Please note that Jekyll generate any fild `file.md` to path `file/index.html`. So the path to the image should be refered to as one level higher.
45 |
46 |
47 | {% endhighlight %}
48 |
49 |
50 |
51 | Please determine the path of the image according to the path of the post itself. Otherwise, an absolute path can be specified,
52 |
53 | ```
54 | 
55 | ```
56 |
57 | where `{{ site.url }}` is the configured url of the site.
58 |
59 |
60 |
61 | ## Notes div
62 |
63 | {% highlight html %}
64 |
65 | Some notes here, with markdown support. markdown="0" will disable markdown support.
66 |
67 |
68 |
69 | This is success text
70 |
71 |
72 |
73 | This is warning text
74 |
75 |
76 |
77 | This is error text
78 |
79 | {% endhighlight %}
80 |
81 |
82 | Please beware that with `markdown="1"` the content and div tags have to be on different lines.
83 |
84 |
85 | Alternatively, we can use the set attributes syntax in kramdown.
86 |
87 | {% highlight md %}
88 | This is a paragraph with some class. The class is specified in the end of the paragraph.
89 | {: .notes--warning}
90 | {% endhighlight %}
91 |
92 | The results shows as a paragraph with the corresponding class. Notice that this only works for one paragraph.
93 |
94 | This is a paragraph with some class. The class is specified in the end of the paragraph.
95 | {: .notes--warning}
96 |
--------------------------------------------------------------------------------
/exampleSite/layouts/index.html:
--------------------------------------------------------------------------------
1 | {{ define "title"}} {{ .Site.Title}} {{end}}
2 | {{ define "header"}} {{ partial "menu" .}} {{end}}
3 |
4 | {{ define "main" }}
5 |
6 | {{ partial "home/hero.html" . }}
7 |
8 | {{ end }}
9 |
10 | {{ define "footer" }} {{ partial "footer" .}} {{ end }}
--------------------------------------------------------------------------------
/exampleSite/layouts/partials/home/hero.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |