Embed about video and update CV

_posts/2020-06-11-borlaugscholar.md → _drafts/2020-06-11-borlaugscholar.md

@@ -1,5 +1,6 @@
 ---
-#layout: post
-title: I'm a Borlaug Scholar!
+layout: post
+title: "I'm a Borlaug Scholar!"
+#date: 2020-06-11
 ---
 The National Association of Plant Breeders has named me one of their 2020 Borlaug Scholars. See the Cornell SIPS announcement <a href="https://blogs.cornell.edu/sips/2020/06/11/hershberger-and-taagen-selected-as-borlaug-scholars/">here</a>.

_posts/2020-12-10-BarbaraMcClintockAward.md → _drafts/2020-12-10-BarbaraMcClintockAward.md

@@ -1,8 +1,10 @@
 ---
-#layout: post
-title: Barbara McClintock Graduate Student Award
+layout: post
+title: 'Barbara McClintock Graduate Student Award'
 ---
 
+[I was awarded the Barbara McClintock Graduate Student Award](https://blogs.cornell.edu/sips/2020/12/17/six-sips-graduate-students-receive-the-barbara-mcclintock-award/) this year along with 5 other stellar plant science graduate students.
+
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">Congrats to Synapsis students Sarah Jensen, Jenna Hershberger <a href="https://twitter.com/jennahersh?ref_src=twsrc%5Etfw">@jennahersh</a>, and Dan Sweeney <a href="https://twitter.com/san_dweeney?ref_src=twsrc%5Etfw">@san_dweeney</a> for winning the Barbara McClintock Graduate Student Award est in 1992 to honor outstanding senior graduate students studying in the Plant Sciences! <a href="https://t.co/pfiYDieh4b">pic.twitter.com/pfiYDieh4b</a></p>&mdash; Cornell Synapsis (@CornellSynapsis) <a href="https://twitter.com/CornellSynapsis/status/1337482070797524994?ref_src=twsrc%5Etfw">December 11, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
 
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">The McClintock award is awarded annually and students are selected based on their academic, research, teaching and outreach achievements as well as on their potential to continue an outstanding career in the Plant Sciences.</p>&mdash; Cornell Synapsis (@CornellSynapsis) <a href="https://twitter.com/CornellSynapsis/status/1337482071950970882?ref_src=twsrc%5Etfw">December 11, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

_drafts/2021-07-19-NIRSbasics.md

@@ -0,0 +1,43 @@
+---
+layout: post
+title: 'NIRS Basics'
+---
+
+Visible and near-infrared spectroscopy (vis-NIRS) can be related to reference phenotypes through statistical models to produce accurate phenotypic predictions for unobserved samples, increasing phenotyping throughput. This technique is commonly used for predicting traits such as total starch, protein, carotenoid, and water content in many plant breeding programs.
+
+[Breedbase](https://breedbase.org) implements the R package [*waves*](https://CRAN.R-project.org/package=waves) to offer training, evaluation, storage, and use of vis-NIRS prediction models for a wide range of spectrometers and phenotypes.
+
+
+# NIRS history
+
+# Plant breeding applications
+
+# Limitations
+
+# Analysis
+## Outlier identification and removal
+## Spectral pretreatments
+## Model algorithms
+## Cross-validation
+## Prediction
+
+# Software options
+* [*waves*](https://CRAN.R-project.org/package=waves)
+* [Unscrambler (CAMO)](https://www.camo.com)
+* [WinISI (Foss)](https://www.fossanalytics.com/en)
+* [OPUS (Brucker)](http://www.bruker.com)
+* many other proprietary options and services
+
+Recommended reading:
+* [Barnes, R.J., M.S. Dhanoa, and S.J. Lister. 1989. Standard normal variate transformation and de-trending of near-infrared diffuse reflectance spectra. Appl. Spectrosc. 43(5): 772-777. doi: 10.1366/0003702894202201](https://doi.org/10.1366%2F0003702894202201)
+* Breiman, L. 2001. Random forests. Mach. Learn. 45: 5-32. doi: 10.1201/9780429469275-8.
+* Ho, T.K. 1995. Random decision forests. Proc. Int. Conf. Doc. Anal. Recognition, ICDAR 1: 278-282. doi: 10.1109/ICDAR.1995.598994.
+* Jarquín, D., C. Lemes da Silva, R.C. Gaynor, J. Poland, A. Fritz, et al. 2017. Increasing Genomic-Enabled Prediction Accuracy by Modeling Genotype x Environment Interactions in Kansas Wheat. Plant Genome 10(2): plantgenome2016.12.0130. doi: 10.3835/plantgenome2016.12.0130.
+* Johnson, R.A., and D.W. Wichern. 2007. Applied Multivariate Statistical Analysis (6th Edition).
+De Maesschalck, R., D. Jouan-Rimbaud, and D.L. Massart. 2000. The Mahalanobis distance. Chemom. Intell. Lab. Syst. 50(1): 1-18. doi: 10.1016/S0169-7439(99)00047-7.
+* Mahalanobis, P.C. 1936. On the generalized distance in statistics. Natl. Inst. Sci. India.
+* Savitzky, A., and M.J.E. Golay. 1964. Smoothing and Differentiation of Data by Simplified Least Squares Procedures. Anal. Chem. 36(8): 1627-1639. doi: 10.1021/ac60214a047.
+* Shrestha, R., L. Matteis, M. Skofic, A. Portugal, G. McLaren, et al. 2012. Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. Front. Physiol. 3 AUG(August): 1-10. doi: 10.3389/fphys.2012.00326.
+* Vapnik, V.N. 2000. The Nature of Statistical Learning Theory. Springer New York, New York, NY.
+* Wold, S., A. Ruhe, H. Wold, and W.J. Dunn, III. 1984. The Collinearity Problem in Linear Regression. The Partial Least Squares (PLS) Approach to Generalized Inverses. SIAM J. Sci. Stat. Comput. 5(3): 735-743. doi: 10.1137/0905052.
+* Wold, S., M. Sjöström, and L. Eriksson. 2001. PLS-regression: a basic tool of chemometrics. Chemom. Intell. Lab. Syst. 58(2): 109-130. doi: 10.1016/S0169-7439(01)00155-1.

_drafts/draft.md

@@ -0,0 +1,14 @@
+---
+#title: DRAFT
+---
+
+<ul style="center">
+	<center><img class="TextWrap" src="/assets/images/about.jpg" alt="Jenna Hershberger" style="width:25%; height:25%; object-fit:cover;border-radius:5%"></center>
+</ul>
+
+<center>
+<ul style="center">
+ <center><iframe width="840" height="500" src="https://s3.amazonaws.com/embed.animoto.com/play.html?w=swf/production/vp1&e=1626193464&f=mMKKimCvKLqVrG649rasaw&d=0&m=p&r=360p+480p+720p&volume=100&start_res=720p&i=m&asset_domain=s3-p.animoto.com&animoto_domain=animoto.com&options=" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
+ </iframe>
+ </ul>
+ </center>

_includes/header.html

@@ -14,7 +14,8 @@ <h1>{{ site.title }}</h1>
 			</div>
 			<nav>
 				<ul>
-					{% for page in site.pages  %}
+					{% assign sorted_pages = site.pages | sort:"order" %}
+					{% for page in sorted_pages %}
 					{% if page.title %}
 					<!-- page.path is: {{ page.path }} -->
 					<li><a href="#{{ page.title }}">{{ page.title }}</a></li>
@@ -25,4 +26,4 @@ <h1>{{ site.title }}</h1>
 		</header>
 
 	<!-- Main -->
-		<div id="main">
+		<div id="main">

_layouts/default.html

@@ -5,7 +5,7 @@
 	Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
 -->
 <html>
-
+{% assign page_name = page.name | replace: '.html','' | replace: '.md','' %}
 {% include head.html %}
 
 

_layouts/post.html

@@ -0,0 +1,31 @@
+<!DOCTYPE HTML>
+<!--
+Forty by HTML5 UP html5up.net | @ajlkn Free for personal
+and commercial use under the CCA 3.0 license (html5up.net/license)
+-->
+<html>
+
+{% include head.html %}
+
+<body>
+
+<!-- Main -->
+<div id="main" class="alt">
+
+<!-- One -->
+<section id="one">
+  <div class="inner">
+    <header class="major">
+      <h1>{{ page.title }}</h1>
+    </header>
+    {% if page.image %}<span class="image main"><img src="{{ site.baseurl }}/{{ page.image }}" alt="" /></span>{% endif %}
+    {{ content }}
+  </div>
+</section>
+
+</div>
+    {% include footer.html %}
+
+</body>
+
+</html>

about.md

@@ -1,10 +1,9 @@
 ---
 title: about
+order: 1
 ---
-
-<ul style="center">
-	<center><img class="TextWrap" src="/assets/images/about.jpg" alt="Jenna Hershberger" style="width:25%; height:25%; object-fit:cover;border-radius:5%"></center>
-</ul>
+<iframe width="420" height="250" style="float:right; margin:0 10px 0 10px" src="https://s3.amazonaws.com/embed.animoto.com/play.html?w=swf/production/vp1&e=1626193464&f=mMKKimCvKLqVrG649rasaw&d=0&m=p&r=360p+480p+720p&volume=100&start_res=720p&i=m&asset_domain=s3-p.animoto.com&animoto_domain=animoto.com&options=" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
+ </iframe>
 
 Welcome! My name is Jenna and I just defended my Ph.D. dissertation in Plant Breeding and Genetics with [Mike Gore's lab](http://blogs.cornell.edu/gorelab/) at Cornell University (June 2021). I study the genetics, genomics, and transcriptomics of sweet corn nutritional quality traits and develop near-infrared spectroscopy-based approaches and analysis tools for the phenotyping of quality traits in cassava. Find out more about my current and past research projects on my [research page](#research).
 

blog.md

@@ -1,12 +1,15 @@
 ---
-layout: default
+#layout: default
 #title: blog
+#excerpt_separator: <!--more-->
+#order: 4
 ---
 
 <ul>
   {% for post in site.posts %}
     <li>
       <a href="{{ post.url }}">{{ post.title }}</a>
+      {{ post.excerpt }}
     </li>
   {% endfor %}
 </ul>

cv.md

@@ -1,4 +1,7 @@
 ---
 title: CV
+order: 2
 ---
-<object data="assets/pdfs/Jenna_M_Hershberger_CV.pdf" width = "100%" height = "700" type="application/pdf"></object>
+<object data="/assets/pdfs/Jenna_M_Hershberger_CV.pdf" width = "100%" height = "700" type="application/pdf"></object>
+
+LaTeX template: <a href ="https://github.com/posquit0/Awesome-CV">Claud D. Park</a>

research.md

@@ -1,6 +1,7 @@
 ---
 title: research
 #image: nacrri.jpg
+order: 3
 ---
 
 I am interested in international agriculture and rural development with a focus on breeding for improved nutritional quality. I want to empower resource-limited plant breeding programs through the development and deployment of appropriate and user-friendly tools for data capture, storage, and reproducible analyses.
@@ -21,7 +22,7 @@ I am interested in international agriculture and rural development with a focus
 </div>
 
 	<h3 class="major">PhenoApps</h3>
-	<p>The <a href="https://phenoapps.org">PhenoApps</a> project is focused on the development of Android apps for the efficient collection of plant phenotypes. Our open-source apps are available for free on <a href="https://play.google.com/store/apps/dev?id=9194692563580469241">Google Play</a> and the source code can be found on <a href="https://github.com/PhenoApps">GitHub</a>. Throughout the project, I have collaborated closely with <a href="https://www.nextgencassava.org/">Nextgen Cassava</a> to explore the use of low-cost near-infrared spectrometers for quality trait prediction in fresh cassava roots. This work led to the creation of a flexible spectral data analysis pipeline in the form of an R package (<i>waves</i>, <a href="https://cran.r-project.org/package=waves">available on CRAN</a>) and <a href="https://www.cassavabase.org/">Cassavabase</a> GUI tool. Both are described in our <a href ="https://doi.org/10.1002/ppj2.20012">recent peer-reviewed manscript in the Plant Phenome Journal</a>. Our team has also developed an Android app, <a href ="https://github.com/PhenoApps/Prospector">Prospector</a>, to improve spectrometer workflows for a breeding program context. We recently released a <a href ="https://arxiv.org/abs/2104.07071">preprint</a> on this work and are in the process of submitting the app to Google Play. This project is made possible by NSF-BREAD <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1543958">IOS-1543958</a> and the USAID under Cooperative Agreement No. 7200AA‐19LE‐00005, <a href ="https://ilci.cornell.edu">the Feed the Future Innovation lab for Crop Improvement</a>.</p>
+	<p>The <a href="https://phenoapps.org">PhenoApps</a> project is focused on the development of Android apps for the efficient collection of plant phenotypes. Our open-source apps are available for free on <a href="https://play.google.com/store/apps/dev?id=9194692563580469241">Google Play</a> and the source code can be found on <a href="https://github.com/PhenoApps">GitHub</a>. Throughout the project, I have collaborated closely with <a href="https://www.nextgencassava.org/">Nextgen Cassava</a> to explore the use of low-cost near-infrared spectrometers for quality trait prediction in fresh cassava roots. This work led to the creation of a flexible spectral data analysis pipeline in the form of an R package (<i>waves</i>, <a href="https://cran.r-project.org/package=waves">available on CRAN</a>) and <a href="https://www.cassavabase.org/">Cassavabase</a> GUI tool. Both are described in our <a href ="https://doi.org/10.1002/ppj2.20012">recent peer-reviewed manscript in the Plant Phenome Journal</a>. Our team has also developed an Android app, <a href ="https://github.com/PhenoApps/Prospector">Prospector</a>, to improve spectrometer workflows for a breeding program context. We recently released a <a href ="https://arxiv.org/abs/2104.07071">preprint</a> on this work and it is also available on <a href ="https://play.google.com/store/apps/details?id=org.phenoapps.prospector">Google Play</a>. This project is made possible by NSF-BREAD <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1543958">IOS-1543958</a> and the USAID under Cooperative Agreement No. 7200AA‐19LE‐00005, <a href ="https://ilci.cornell.edu">the Feed the Future Innovation lab for Crop Improvement</a>.</p>
 </section>
 
 <hr />
@@ -40,7 +41,7 @@ I am interested in international agriculture and rural development with a focus
 </div>
 
 	<h3 class="major">Sweet corn nutritional quality</h3>
-	<p>In 2019, I was awarded a USDA NIFA AFRI EWD Predoctoral fellowship titled <i>Integrating transcriptomics for the improvement of genetic dissection and prediction of provitamin A and vitamin E in fresh sweet corn kernels</i>. Last summer, I grew out a panel of diverse sweet corn inbred lines and harvested fresh kernels for RNA-seq. RNA has been extracted and we're now analyzing the sequences to study the control of carotenoid and tocochromanol traits through TWAS and transcriptome prediction.</p>
+	<p>In 2019, I was awarded a USDA NIFA AFRI EWD Predoctoral fellowship titled <i>Integrating transcriptomics for the improvement of genetic dissection and prediction of provitamin A and vitamin E in fresh sweet corn kernels</i>. Last summer, I grew out a panel of diverse sweet corn inbred lines and harvested fresh kernels for RNA-seq. RNA has been extracted and we're now analyzing the sequenced transcripts to study the control of carotenoid and tocochromanol traits through transcriptome-wide association and prediction.</p>
 </section>
 
 <hr />
@@ -62,4 +63,10 @@ I am interested in international agriculture and rural development with a focus
 	<p>During my time in the <a href="https://vcru.wisc.edu/simon/">Simon Lab</a> at UW-Madison, I worked on the first iteration of the USDA NIFA OREI <a href="https://eorganic.info/carrotimprovement/about"><i>Carrot Improvement for Organic Agriculture</i></a> project. I was involved in every stage of the carrot breeding program, from planting and cage building for fly pollination to DNA extraction, HPLC prep, and tissue culture, and loved every part of it. It's safe to say that my experience with the carrot group inspired me to pursue a graduate education in plant breeding and genetics. My family likes to joke that the true start of my career was my (single line) speaking part in a BigTen Network special on breeding carrots for color and flavor. Watch the video <a href="https://www.youtube.com/embed/ZV2F4HjT8qM"><i>here</i></a> and judge for yourself! &#8681;
   </p>
 
+  <ul style="center">
+   <center><iframe width="840" height="500" src="https://www.youtube.com/embed/ZV2F4HjT8qM" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
+   </iframe>
+   </center>
+ </ul>
+
 </section>

resources.md

@@ -2,5 +2,5 @@
 #title: Resources
 ---
 
-* If you ever find yourself in Southern Indiana, I highly recommend visiting the [Hartman Arboretum](https://www.hartmanarboretum.org/). They also have a great [instagram account]()
+* If you ever find yourself in Southern Indiana, I highly recommend visiting the [Hartman Arboretum](https://www.hartmanarboretum.org/). They also have a great [instagram account](https://www.instagram.com/hartman_arboretum/)
 *