Skip to content

Commit

Permalink
Render bookdown
Browse files Browse the repository at this point in the history
  • Loading branch information
@jhudsl-robot
jhudsl-robot committed Feb 1, 2024
1 parent 3bb88e3 commit 9ba6a75
Show file tree
Hide file tree
Showing 18 changed files with 634 additions and 83 deletions.
36 changes: 4 additions & 32 deletions docs/01-BioDIGS_project_overview.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

# Background

One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers <sup>1</sup>. It can also lead to improved scientific reasoning and increased academic performance overall <sup>2</sup>. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science <sup>3</sup> <sup>4</sup>.
One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers [@Russell2007]. It can also lead to improved scientific reasoning and increased academic performance overall [@Buffalari2020]. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science [@Canner2017; @GDSCN2022].

The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education.

Expand All @@ -28,38 +28,10 @@ The genome assembly and analyses for BioDIGS have been done using the NHGRI [AnV

## Why soil microbes?

It can be challenging to include undergraduates in human genomic and health research, especially in a classroom context. Both human genetic data and human health data are protected data, which limits the sort of information students can access without undergoing specialized ethics training. However, the same sorts of data cleaning and analysis methods used for human genomic data are also used for microbial genomic data, which does not have the same sort of legal protections as human genetic data. This makes it ideal for training undergraduate students at the beginning of their careers and can be used to prepare students for future research in human genomics and health <sup>5</sup>. Additionally, the microbes in the soil can have big impacts on our health <sup>6</sup>.
It can be challenging to include undergraduates in human genomic and health research, especially in a classroom context. Both human genetic data and human health data are protected data, which limits the sort of information students can access without undergoing specialized ethics training. However, the same sorts of data cleaning and analysis methods used for human genomic data are also used for microbial genomic data, which does not have the same sort of legal protections as human genetic data. This makes it ideal for training undergraduate students at the beginning of their careers and can be used to prepare students for future research in human genomics and health [@Jurkowski2017]. Additionally, the microbes in the soil can have big impacts on our health [@BrevikBurgess2014].

## Heavy metals and human health

Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals <sup>7</sup>. When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations <sup>8</sup> <sup>9</sup>. Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas <sup>10</sup>.
Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals [@Yan2020]. When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations [@Khan2023; @Wang2022]. Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas [@Jones2022].

Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers <sup>11</sup> <sup>12</sup> <sup>13</sup>.

## References

1: Russell et al. 2007: [https://doi.org/10.1126/science.1140384](https://doi.org/10.1126/science.1140384)

2: Buffalari et al. 2020: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040836/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040836/)

3: Canner et al. 2017: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398168/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398168/)

4: GDSCN 2022: [https://doi.org/10.1101/gr.276496.121](https://doi.org/10.1101/gr.276496.121)

5: Jurkowski et al. 2007: [https://doi.org/10.1187/cbe.07-09-0075](https://doi.org/10.1187/cbe.07-09-0075)

6: Brevik and Burgess 2004: [https://www.nature.com/scitable/knowledge/library/the-influence-of-soils-on-human-health-127878980/](https://www.nature.com/scitable/knowledge/library/the-influence-of-soils-on-human-health-127878980/)

7: Yan et al. 2020: [https://doi.org/10.1016/j.scitotenv.2019.136116](https://doi.org/10.1016/j.scitotenv.2019.136116)

8: Khan et al. 2023: [https://pubmed.ncbi.nlm.nih.gov/36907936/](https://pubmed.ncbi.nlm.nih.gov/36907936/)

9: Wang et al. 2022: [https://pubmed.ncbi.nlm.nih.gov/35240153/](https://pubmed.ncbi.nlm.nih.gov/35240153/)

10: Jones et al. 2022: {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8834334/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8834334/)

11: Gorovtsov et al. 2018: [https://doi.org/10.1007/s11356-018-1465-9](https://doi.org/10.1007/s11356-018-1465-9)

12: Nguyen et al. 2019: [https://doi.org/10.1007/s11783-019-1129-0](https://doi.org/10.1007/s11783-019-1129-0)

13: Sun et al. 2021: [https://doi.org/10.1016/j.jenvman.2021.113754](https://doi.org/10.1016/j.jenvman.2021.113754)
Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers [@Gorovtsov2018; @Nguyen2019; @Sun2021].
26 changes: 24 additions & 2 deletions docs/404.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@



<meta name="date" content="2024-01-31" />
<meta name="date" content="2024-02-01" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -65,6 +65,28 @@



<style type="text/css">
/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}
</style>

<link rel="stylesheet" href="assets/style.css" type="text/css" />
<link rel="stylesheet" href="assets/GDSCN_style/gdscn.css" type="text/css" />
Expand Down Expand Up @@ -97,7 +119,6 @@
<li class="chapter" data-level="1.3" data-path="background.html"><a href="background.html#what-is-cloud-computing"><i class="fa fa-check"></i><b>1.3</b> What is cloud computing?</a></li>
<li class="chapter" data-level="1.4" data-path="background.html"><a href="background.html#why-soil-microbes"><i class="fa fa-check"></i><b>1.4</b> Why soil microbes?</a></li>
<li class="chapter" data-level="1.5" data-path="background.html"><a href="background.html#heavy-metals-and-human-health"><i class="fa fa-check"></i><b>1.5</b> Heavy metals and human health</a></li>
<li class="chapter" data-level="1.6" data-path="background.html"><a href="background.html#references"><i class="fa fa-check"></i><b>1.6</b> References</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
<ul>
Expand Down Expand Up @@ -176,6 +197,7 @@
</ul></li>
</ul></li>
<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
<li class="chapter" data-level="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
Expand Down
2 changes: 1 addition & 1 deletion docs/About.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ These credits are based on our [course contributors table guidelines](https://gi
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-01-31
## date 2024-02-01
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
Expand Down
2 changes: 2 additions & 0 deletions docs/References.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@

# References
34 changes: 28 additions & 6 deletions docs/about-the-authors.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,15 +23,15 @@



<meta name="date" content="2024-01-31" />
<meta name="date" content="2024-02-01" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black" />

<link rel="shortcut icon" href="assets/GDSCN_style/gdscn_favicon.ico" type="image/x-icon" />
<link rel="prev" href="student-guide.html"/>

<link rel="next" href="references.html"/>
<script src="libs/header-attrs-2.10/header-attrs.js"></script>
<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/fuse.min.js"></script>
Expand Down Expand Up @@ -65,6 +65,28 @@



<style type="text/css">
/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}
</style>

<link rel="stylesheet" href="assets/style.css" type="text/css" />
<link rel="stylesheet" href="assets/GDSCN_style/gdscn.css" type="text/css" />
Expand Down Expand Up @@ -97,7 +119,6 @@
<li class="chapter" data-level="1.3" data-path="background.html"><a href="background.html#what-is-cloud-computing"><i class="fa fa-check"></i><b>1.3</b> What is cloud computing?</a></li>
<li class="chapter" data-level="1.4" data-path="background.html"><a href="background.html#why-soil-microbes"><i class="fa fa-check"></i><b>1.4</b> Why soil microbes?</a></li>
<li class="chapter" data-level="1.5" data-path="background.html"><a href="background.html#heavy-metals-and-human-health"><i class="fa fa-check"></i><b>1.5</b> Heavy metals and human health</a></li>
<li class="chapter" data-level="1.6" data-path="background.html"><a href="background.html#references"><i class="fa fa-check"></i><b>1.6</b> References</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
<ul>
Expand Down Expand Up @@ -176,6 +197,7 @@
</ul></li>
</ul></li>
<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
<li class="chapter" data-level="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
Expand Down Expand Up @@ -354,7 +376,7 @@ <h1>About the Authors</h1>
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-01-31
## date 2024-02-01
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
Expand Down Expand Up @@ -426,8 +448,8 @@ <h1>About the Authors</h1>
</div>
</div>
</div>
<a href="student-guide.html" class="navigation navigation-prev navigation-unique" aria-label="Previous page"><i class="fa fa-angle-left"></i></a>

<a href="student-guide.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
<a href="references.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
</div>
</div>
<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
Expand Down
26 changes: 24 additions & 2 deletions docs/anvil-workspace.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@



<meta name="date" content="2024-01-31" />
<meta name="date" content="2024-02-01" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -65,6 +65,28 @@



<style type="text/css">
/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}
</style>

<link rel="stylesheet" href="assets/style.css" type="text/css" />
<link rel="stylesheet" href="assets/GDSCN_style/gdscn.css" type="text/css" />
Expand Down Expand Up @@ -97,7 +119,6 @@
<li class="chapter" data-level="1.3" data-path="background.html"><a href="background.html#what-is-cloud-computing"><i class="fa fa-check"></i><b>1.3</b> What is cloud computing?</a></li>
<li class="chapter" data-level="1.4" data-path="background.html"><a href="background.html#why-soil-microbes"><i class="fa fa-check"></i><b>1.4</b> Why soil microbes?</a></li>
<li class="chapter" data-level="1.5" data-path="background.html"><a href="background.html#heavy-metals-and-human-health"><i class="fa fa-check"></i><b>1.5</b> Heavy metals and human health</a></li>
<li class="chapter" data-level="1.6" data-path="background.html"><a href="background.html#references"><i class="fa fa-check"></i><b>1.6</b> References</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
<ul>
Expand Down Expand Up @@ -176,6 +197,7 @@
</ul></li>
</ul></li>
<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
<li class="chapter" data-level="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
<li class="divider"></li>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
Expand Down
Loading

0 comments on commit 9ba6a75

Please sign in to comment.