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draft of playground
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ktmeaton committed May 20, 2020
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54 changes: 41 additions & 13 deletions narratives/DHSI2020Local.md
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<!-- Exhibit Format -->
<!----------------------------------------------------------------------------->

# [Exhibit Format](http://localhost:4000/cui2013Local?m=num_date&s=GCA_000013825.1_ASM1382v1_genomic)
<!----------------------------------------------------------------------------->
# [Exhibit](http://localhost:4000/cui2013Local?m=num_date&s=GCA_000013825.1_ASM1382v1_genomic)

## Narrative Text
---

#### This demonstration explores a special form of a digital narrative. Scrollable text is presented in the left-side panel, with exhibit items and contextual images presented in the right-side panel.

Expand All @@ -54,7 +55,10 @@ This is the exhibit abstract section.
```

# [Exhibit Data](http://localhost:4000/cui2013Local?m=num_date)
<!----------------------------------------------------------------------------->
# [Exhibit](http://localhost:4000/cui2013Local?m=num_date)

---

#### The exhibit objects here are samples of the plague bacterium, *Yersinia pestis*.

Expand All @@ -66,41 +70,63 @@ This is the exhibit abstract section.

#### Through this analysis... purpose and questions....

---

## Digital Exhibits

* Built and powered by [NextStrain](https://nextstrain.org/).
* Similar to [StoryMap](https://storymaps-classic.arcgis.com/en/).
#### Built and powered by [NextStrain](https://nextstrain.org/).
#### Digital Humanities Parallels: [StoryMap](https://storymaps-classic.arcgis.com/en/).

<!----------------------------------------------------------------------------->
<!-- Idea Playground -->
<!----------------------------------------------------------------------------->

# [Playground of Ideas 1](http://localhost:4000/cui2013Local?m=num_date)
<!----------------------------------------------------------------------------->
# [Playground of Ideas](http://localhost:4000/cui2013Locall?d=map&p=full)

## Heading
---

#### Writing
## <b>Investigating Bias</b>

# [Playground of Ideas 2](http://localhost:4000/cui2013Local)
#### Exhibits can be a powerful platform for discovering underlying problems and asking new questions.

## Compare and Contextualize
#### Recent human plague cases occurred most frequently in Madagascar, Congo, and Uganda.

#### [Compare Datasets](http://localhost:4000/morelli2010Local:cui2013Local?c=BioSampleGeographicLocation&m=num_date).
<a href="https://www.economist.com/graphic-detail/2017/07/05/the-return-of-the-plague">
<img src="https://www.economist.com/img/b/1280/757/85/sites/default/files/20170708_WOM968_0.png" width="80%">
<p style='text-align: center;'>Reported Human Plague Cases (2010-2015)</p>
</a>

Example: Highlight the major increase in China samples.
Also, deeper window into the past.
#### Yet the DNA plague samples analyzed here don't reflect that. Instead there is a strong geographic bias towards samples collected in China.

#### [Compare disease networks by study (2010 vs. 2013)](http://localhost:4000/morelli2010Local:cui2013Local?c=BioSampleGeographicLocation&m=num_date).

<!----------------------------------------------------------------------------->
# [Playground of Ideas](http://localhost:4000/cui2013Local?d=map&m=num_date&p=full&animate=1300-01-01,2006-01-01,1,0,30000)

---

## <b>Compare and Contextualize</b>

#### How do the results here on a spread reconstruction compare to historical reconstructions from archival documents?

<a href="https://doi.org/10.13140/RG.2.2.25362.25281">
<img src="https://www.researchgate.net/profile/Anne_Laudisoit2/publication/315837122/figure/fig1/AS:652961457897473@1532689551350/a-leftThe-origin-and-spread-of-Justinian-plague.png" width="80%">
<p style='text-align: center;'>Origins and Spread of the Plague</p>
</a>

<!----------------------------------------------------------------------------->
<!-- Interdisciplinary -->
<!----------------------------------------------------------------------------->

<!----------------------------------------------------------------------------->
# [Interdisciplinary 1](http://localhost:4000/cui2013Local?d=map&m=num_date&p=full&animate=1300-01-01,2006-01-01,1,0,30000)

## Archival Work

Biraben Plague Documents

<!----------------------------------------------------------------------------->
# [Interdisciplinary 2](http://localhost:4000/cui2013Local?c=BioSampleHost&legend=open)

## Ecology
Expand All @@ -111,6 +137,7 @@ Cute Pictures of Rodents
<!-- Publish In Place -->
<!----------------------------------------------------------------------------->

<!----------------------------------------------------------------------------->
# [Publish in Place](http://localhost:4000/cui2013Local)

## Heading
Expand All @@ -121,6 +148,7 @@ Writing
<!-- Conclusion -->
<!----------------------------------------------------------------------------->

<!----------------------------------------------------------------------------->
# [Conclusion](http://localhost:4000/cui2013Local)

## Heading
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54 changes: 41 additions & 13 deletions narratives/plague-phylogeography_DHSI2020Remote.md
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,10 @@ This is the exhibit abstract section.
<!-- Exhibit Format -->
<!----------------------------------------------------------------------------->

# [Exhibit Format](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?m=num_date&s=GCA_000013825.1_ASM1382v1_genomic)
<!----------------------------------------------------------------------------->
# [Exhibit](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?m=num_date&s=GCA_000013825.1_ASM1382v1_genomic)

## Narrative Text
---

#### This demonstration explores a special form of a digital narrative. Scrollable text is presented in the left-side panel, with exhibit items and contextual images presented in the right-side panel.

Expand All @@ -54,7 +55,10 @@ This is the exhibit abstract section.
```

# [Exhibit Data](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?m=num_date)
<!----------------------------------------------------------------------------->
# [Exhibit](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?m=num_date)

---

#### The exhibit objects here are samples of the plague bacterium, *Yersinia pestis*.

Expand All @@ -66,41 +70,63 @@ This is the exhibit abstract section.

#### Through this analysis... purpose and questions....

---

## Digital Exhibits

* Built and powered by [NextStrain](https://nextstrain.org/).
* Similar to [StoryMap](https://storymaps-classic.arcgis.com/en/).
#### Built and powered by [NextStrain](https://nextstrain.org/).
#### Digital Humanities Parallels: [StoryMap](https://storymaps-classic.arcgis.com/en/).

<!----------------------------------------------------------------------------->
<!-- Idea Playground -->
<!----------------------------------------------------------------------------->

# [Playground of Ideas 1](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?m=num_date)
<!----------------------------------------------------------------------------->
# [Playground of Ideas](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remotel?d=map&p=full)

## Heading
---

#### Writing
## <b>Investigating Bias</b>

# [Playground of Ideas 2](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote)
#### Exhibits can be a powerful platform for discovering underlying problems and asking new questions.

## Compare and Contextualize
#### Recent human plague cases occurred most frequently in Madagascar, Congo, and Uganda.

#### [Compare Datasets](https://nextstrain.org/community/ktmeaton/plague-phylogeography/morelli2010Local:community/ktmeaton/plague-phylogeography/cui2013Local?c=BioSampleGeographicLocation&m=num_date).
<a href="https://www.economist.com/graphic-detail/2017/07/05/the-return-of-the-plague">
<img src="https://www.economist.com/img/b/1280/757/85/sites/default/files/20170708_WOM968_0.png" width="80%">
<p style='text-align: center;'>Reported Human Plague Cases (2010-2015)</p>
</a>

Example: Highlight the major increase in China samples.
Also, deeper window into the past.
#### Yet the DNA plague samples analyzed here don't reflect that. Instead there is a strong geographic bias towards samples collected in China.

#### [Compare disease networks by study (2010 vs. 2013)](https://nextstrain.org/community/ktmeaton/plague-phylogeography/morelli2010Local:community/ktmeaton/plague-phylogeography/cui2013Local?c=BioSampleGeographicLocation&m=num_date).

<!----------------------------------------------------------------------------->
# [Playground of Ideas](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?d=map&m=num_date&p=full&animate=1300-01-01,2006-01-01,1,0,30000)

---

## <b>Compare and Contextualize</b>

#### How do the results here on a spread reconstruction compare to historical reconstructions from archival documents?

<a href="https://doi.org/10.13140/RG.2.2.25362.25281">
<img src="https://www.researchgate.net/profile/Anne_Laudisoit2/publication/315837122/figure/fig1/AS:652961457897473@1532689551350/a-leftThe-origin-and-spread-of-Justinian-plague.png" width="80%">
<p style='text-align: center;'>Origins and Spread of the Plague</p>
</a>

<!----------------------------------------------------------------------------->
<!-- Interdisciplinary -->
<!----------------------------------------------------------------------------->

<!----------------------------------------------------------------------------->
# [Interdisciplinary 1](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?d=map&m=num_date&p=full&animate=1300-01-01,2006-01-01,1,0,30000)

## Archival Work

Biraben Plague Documents

<!----------------------------------------------------------------------------->
# [Interdisciplinary 2](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote?c=BioSampleHost&legend=open)

## Ecology
Expand All @@ -111,6 +137,7 @@ Cute Pictures of Rodents
<!-- Publish In Place -->
<!----------------------------------------------------------------------------->

<!----------------------------------------------------------------------------->
# [Publish in Place](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote)

## Heading
Expand All @@ -121,6 +148,7 @@ Writing
<!-- Conclusion -->
<!----------------------------------------------------------------------------->

<!----------------------------------------------------------------------------->
# [Conclusion](https://nextstrain.org/community/ktmeaton/plague-phylogeography/cui2013Remote)

## Heading
Expand Down

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