From efdffa526223c46ce6181378bba63638c5ef0171 Mon Sep 17 00:00:00 2001 From: Jenna Hershberger Date: Mon, 19 Jul 2021 12:28:28 -0500 Subject: [PATCH] Embed about video and update CV --- .../2020-06-11-borlaugscholar.md | 5 +- .../2020-12-10-BarbaraMcClintockAward.md | 6 ++- _drafts/2021-07-19-NIRSbasics.md | 43 ++++++++++++++++++ _drafts/draft.md | 14 ++++++ _includes/header.html | 5 +- _layouts/default.html | 2 +- _layouts/post.html | 31 +++++++++++++ about.md | 7 ++- assets/pdfs/Jenna_M_Hershberger_CV.pdf | Bin 65369 -> 66084 bytes blog.md | 5 +- cv.md | 5 +- research.md | 11 ++++- resources.md | 2 +- 13 files changed, 120 insertions(+), 16 deletions(-) rename {_posts => _drafts}/2020-06-11-borlaugscholar.md (79%) rename {_posts => _drafts}/2020-12-10-BarbaraMcClintockAward.md (81%) create mode 100644 _drafts/2021-07-19-NIRSbasics.md create mode 100644 _drafts/draft.md create mode 100644 _layouts/post.html diff --git a/_posts/2020-06-11-borlaugscholar.md b/_drafts/2020-06-11-borlaugscholar.md similarity index 79% rename from _posts/2020-06-11-borlaugscholar.md rename to _drafts/2020-06-11-borlaugscholar.md index 6bc1b46e..91a9c109 100644 --- a/_posts/2020-06-11-borlaugscholar.md +++ b/_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 here. diff --git a/_posts/2020-12-10-BarbaraMcClintockAward.md b/_drafts/2020-12-10-BarbaraMcClintockAward.md similarity index 81% rename from _posts/2020-12-10-BarbaraMcClintockAward.md rename to _drafts/2020-12-10-BarbaraMcClintockAward.md index 380ba53c..ba6c4fdf 100644 --- a/_posts/2020-12-10-BarbaraMcClintockAward.md +++ b/_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. +

Congrats to Synapsis students Sarah Jensen, Jenna Hershberger @jennahersh, and Dan Sweeney @san_dweeney for winning the Barbara McClintock Graduate Student Award est in 1992 to honor outstanding senior graduate students studying in the Plant Sciences! pic.twitter.com/pfiYDieh4b

— Cornell Synapsis (@CornellSynapsis) December 11, 2020

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.

— Cornell Synapsis (@CornellSynapsis) December 11, 2020
diff --git a/_drafts/2021-07-19-NIRSbasics.md b/_drafts/2021-07-19-NIRSbasics.md new file mode 100644 index 00000000..41bba3bf --- /dev/null +++ b/_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. diff --git a/_drafts/draft.md b/_drafts/draft.md new file mode 100644 index 00000000..8c09d912 --- /dev/null +++ b/_drafts/draft.md @@ -0,0 +1,14 @@ +--- +#title: DRAFT +--- + + + +
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