Current Topics and Methods Courses

Current Topics and Methods Courses

Autumn 2018

HCS 7194

Genome Analytics 

Instructor: Jonathan Fresnedo, fresnedoramirez.1@osu.edu

14 weeks, 3 credits

Meeting Time: Tuesday 1:50 PM – 2:45 PM and Thursday 1:50 PM - 4:35 PM 

Location: Williams 117A and Selby 203, Wooster campus

Class Numbers: 35346-35347

55 minutes lecture on Tuesday, 55 minutes lecture and 1:5 hr Lab on Thursday 

the Genome Analytics course is to facilitate a hands-on analytical and quantitative approach for graduate students to learn about the basic pipelines for the data analysis of genomic sequences, focusing on incorporating these bioinformatics pipelines into their research. This course provides students with the basic concepts for the subsequent broad survey of the latest advances and applications on topics related to genomic sciences and bioinformatics and their implementation in biological sciences, particularly ag-related disciplines. Students will have access to computing resources from the Ohio Supercomputer Center and GitHub repositories.

The main topics that will be approached are:

  • Command line
  • Introduction to the analysis of sequencing data
  • Genome assembly
  • Gene expression
  • Variant calling
  • Metagenomics and microbiomes
  • Epigenetics

 

HCS 8830

Current Topics in Metabolomics

Instructor: Jessica Cooperstone, cooperstone.1@osu.edu

First 7-week; 1 credit 

Meeting time: TBA

Location: TBA

This journal club will focus on critically reviewing and evaluating recent publications in metabolomics, with a focus on applications in plants, foods and human health. The goals of this course are to increase student familiarity with reading and interpreting the metabolomics literature, and to understand ways in which metabolomics may be a useful approach to students’ research.  

HCS 7806

Using Multimedia to Communicate Science to the Public

Instructor: Leah McHale, mchale.21@osu.edu

Second 7-week session; 1 credit

Meeting time: TBA

Class #: TBA

This course is aimed at graduate students seeking to further their science communication abilities. Primarily, students will work collaboratively to create multi-media content aimed at the general public and communicating a topic related to plant science or food production. There will be the opportunity to host these media on HCS websites including the departmental website and Ohio State’s Plant Breeding website.

 

Summer 2018

HCS 8830 

Senescence of Plant Organs

Instructor: Joe Scheerens, scheerens.1@osu.edu

Second 8 week session  

Class #: 20665 (Columbus) and 20666 (Wooster)

 

Spring 2018

HCS 8830 

Plant hormone signal transduction mechanism

Instructor: JC Jang, jang.40@osu.edu

7 Weeks 

Topics of presentation: Abscisic Acid (ABA), Auxin, Brassinosteroids (BRs), Cytokinins (CKs), Ethylene, Gibberellins, Methyl Jasmonates, Peptide hormones, Salicylic Acid (SA), and Stringolactones.

 

Autumn 2017 

HCS 7806 

Introduction to concepts of Bayesian Statistics 

Instructor: Jonathan Fresnedo, fresnedoramirez.1@osu.edu
First 7-week session 
Meeting Time: Tuesday and Thursday 3:00 PM - 5:00 PM Williams 117A
Class Number: 35457
2 hr lecture on Tuesday and 2 hr Lab on Thursday 

This course will provide an overview about methods of Bayesian statistical inference. The class has a humble objective: that students learn (or are at least become aware) of the vocabulary, terminology and concepts regarding this type of statistical inference, which has increasingly grown in popularity in scientific literature. Explanations to the terms and concepts, as well as some hands-on data processing will be included. Calculations would not be the core of the course; however, the analysis of datasets using R, JAGS and Stan are going to be covered during the labs.  The evaluation will be based on quizzes.
 
It is recommended that students interested in the class have already taken a course of basic statistical methods (experimental design is not necessarily but a course on descriptive statistics is required) and have some experience with the Statistical Language R.

The main topics that will be approached are:

  • Refresh of probabilistic distributions
  • Bayesian inference,
    • Linear models
    • Model comparison
  • Application and introduction to Markov chain monte Carlo (MCMC)
  • Introduction to categorical/count models
  • Introduction to hierarchical models
     

 

HCS 7806

Small Plot Research Methods and Equipment

Instructor: Laura Lindsey, lindsey.233@osu.edu
Autumn 2017 Second 7-week session 
Meeting time: TBA
Class #: TBA

(Since we will be using equipment, the course will be Columbus only located off-campus at the Agronomy Shop)
Description: The purpose of this methods course is to discuss small plot research methods for agronomic crops. Students will learn about basic equipment maintenance, how the research equipment works, and have the opportunity to harvest soybeans and plant wheat.

Summer 2017

HCS 7806

Extraction, Separation, Identification, and Quantification of Plant Compounds

Instructors: Joe Scheerens, scheerens.1@osu.edu and Josh Blakeslee, blakeslee.19@osu.edu
Full Term Summer semester, 2 credits
Meeting time: TBA
Class #: TBA
 
*Due to the nature of the lab portion of this course, Columbus based students will enroll in the Wooster listing of the course and travel to Wooster for in-person lecture and lab. 
 
In this course, students will learn to apply specific techniques and equipment for extracting, identifying and quantifying plant compounds with an emphasis on secondary products.  Upon completion, they will
appreciate theoretical and practical aspects of chromatography (TLC, GC, HPLC, FPLC) and electrophoresis, as well as spectrophotometric assays designed to measure purity and activity of extracted compounds.  They will also understand how tissue, cell, organelle complexity affects extraction of desired compounds and recognize optimal choices to maximize yields and purity of desired compounds.  The importance of sampling error and how to minimize it; and the importance of both replication and the use of proper controls (e.g., internal and external standards) will also be emphasized.
 

HCS 8830

Instructor: Joe Scheerens, scheerens.1@osu.edu
Summer 2017 8-Week Session 2 
Meeting Time: TBA
 

HCS 8830 

Instrcutor: Doug Doohan, doohan.1@osu.edu
Summer 2017 8-Week Session 2 
Class numbers: 23011 (Columbus), 23012  (Wooster)
Meeting Time: TBA
This course is designed to meet the needs of current graduate students interested in characterizing soil communities as they relate to soil health.  Goals for the course will include 1) increase student familiarity with the significant biological questions being addressed in the field as well as methods used and 2) improve student critical thinking skills and ability to critically evaluate published works.  
 
 

Spring 2017

HCS 7806

Using Multimedia to Communicate Science to the Public

Instructor: Leah McHale, mchale.21@osu.edu
Spring 2017 Second 7-week session; 1 credit
Meeting time: TBA
Class #: 32260 (Columbus) or 32261 (Wooster)
 
This course is aimed at graduate students seeking to further their science communication abilities. Primarily, students will create visual content aimed at the general public and communicating a topic related to plant science or food production. These media will be hosted on Ohio State’s Plant Breeding website and students will work collaboratively to update the site content.
 
Learning Objectives and Outcomes:
  • Short videos communicating an aspect of plant science or food production
    • Learn how to properly plan, execute, and edit videos
    • Design an independent project and collaborate with other students’ projects
  • Development of Ohio State’s Plant Breeding website:
    • Invite relevant faculty
    • Learn how to edit web content using Drupal
  • Create web content for Ohio State’s Plant Breeding website
    • Videos and infographics
    • Educational pages about plant breeding/genetics

 

HCS 7806

Multivariate Methods using SAS and R

Instructor: Dave Barker, barker.169@osu.edu
Full term, Spring 2017 
Meeting time: Mondays 2:00 PM - 5:00 PM 
Class #s: 29580 (Columbus), 29994 (Wooster) 
1 hr lecture per week; 2 hr Lab

You should have taken a prior statistics class.
 

Meeting time and location:

  • Mon (lecture) 2-3pm; Mon (lab) 3-5pm, video-link to Wooster
  • Howlett 139; Gourley 102
Course will cover a brief survey of multivariate analysis of biological data. This will be a hands-on course using SAS & R and will be of greatest benefit for students with their own data [this will work best with a data matrix of 20-200 rows (individual plots/cases) and 5-20 columns (observations on the same plot/case) – no missing data].
Students will need a laptop with SAS and/or R for the recitation

 

HCS 8830

Principles and Applications of Plant Hormone Signal Transduction Mechanisms

Instructor: JC Jang, jang.40@osu.edu
Spring 2017 Second 7-week session 
Meeting time: TBA
Class #s: 30962, 30963 (Wooster)
 

HCS 8830

Crop Mythbusters- What Works and What Doesn't

Instrcutor: Laura Lindsey, lindsey.233@osu.edu
Spring 2017 Second 7-week session
Meeting time: TBA
Class #s:
We'll discuss non-traditional farming practices and determine if they are supported by the current literature.