Education

Genome Academy

Genome Academy

The IGSP Office of Education & Training is pleased to offer a variety of free, non-credit Genome Academy workshops and seminars open to faculty, staff, students, and trainees. We offer two types of workshops/seminars: 1) tutorials to introduce or enhance research skills or knowledge in genome sciences and policy; and 2) career and professional development workshops to discuss opportunities in science, medicine, and policy. Please see schedules below for current and past Genome Academy offerings. Registration is required for all seminars and workshops - register early to secure your spot! Please contact Jessica Rowland with any questions or suggestions for future Genome Academy offerings.

Spring 2013 Genome Academy

Genome Sciences & Policy Offerings

Course Title: “Qualitative and Quantitative Proteomic Analyses using Mass Spectrometry"

Instructor: M. Arthur Moseley, PhD, Associate Research Professor & Director, Duke Proteomics Core Facility

Course Description: This 3-part course is designed for scientists who want to learn specific techniques for the characterization of peptides and proteins using a variety of mass spectrometric techniques. The course will address fundamental aspects of protein chemistry, sample preparation, mass spectrometry (hardware and software), peptide fragmentation, and sample introduction systems including nanospray, capillary LC, and multi-dimensional LC. Real-world examples of the application of these techniques will include characterization of intact proteins, characterization of post-translational modifications (with emphasis on phosphorylation), identification of proteins via database searching, direct identification of proteins from gels and complex mixtures, and quantitative differential protein expression studies. The role of MS-based methods in interdisciplinary efforts to solve complex biomedical problems will also be addressed. Additionally, there will be tutorials on the use of open source proteomic software tools for interpretation of proteomic datasets.

Date
“Qualitative and Quantitative Proteomic Analyses using Mass Spectrometry"
3/27

Part I: "Fundamentals of Protein Chemistry and Mass Spectrometry"
Video recording of Part I.
4/3

Part II: "Fundamentals of Protein and Peptide Analyses by Mass Spectrometry"
Video recording of Part II.
4/17

Part III: "Differential Expression Proteomics"
Video recording of Part III.
 

Career & Professional Development Offerings

Date
"Science & Health Career Explorations Dinner Series"
3/26

"Science & Health Career Explorations Dinner Series: PHYSICIAN, PHYSICIAN/RESEARCHER: MD, MD/PhD"
Perkins Library 218, 6:00 pm - 7:30 pm. Registration required. Contact jessica.rowland@duke.edu with any questions.
4/2

"Science & Health Career Explorations Dinner Series: SCIENCE COMMUNICATIONS & MEDIA"
Perkins Library 218, 6:00 pm - 7:30 pm. Registration required. Contact jessica.rowland@duke.edu with any questions.
4/9 "Science & Health Career Explorations Dinner Series: SCIENCE, HEALTH & LAW"
Perkins Library 218, 6:00 pm - 7:30 pm. Registration required. Contact jessica.rowland@duke.edu with any questions.
 

Fall 2012 Genome Academy

Genome Sciences & Policy Offerings

Date "Introduction to Unix"
10/2

Introduction to Unix - Unit 1: In the Beginning
This class unit will be a basic introduction to the history of Unix/Linux, as well as an introduction to the students in the class and the teachers. We will also cover basic login and how to access servers remotely using SSH. Teer Building 106, 9 am - 10 am.
10/2

Introduction to Unix - Unit 2: Where am I and what am I doing here?
Once logged in, we will really get to work. This unit will cover many basic filesystem operations. Users will be able to navigate the various file system paths, learn where many common items are located, and how to interact with files based on permissions. Teer Building 106, 10:15 am - 11:15 am.
10/4 Introduction to Unix - Unit 3: Where is my stuff and how do I manage it?
Continuing from where we left off in the previous session, this one will cover how to further interact with files and directories, including gathering storage information, how and where you store your data, to read, edit, and save your files, including archiving. Teer Building 106, 9 am - 10 am.
10/4

Introduction to Unix - Unit 4: How can I transfer my stuff? (To infinity and beyond)
This unit will deal with transferring data from one directory to another across servers, and across the internet, including methods to backup your data and secure its movement and transfer. Finally we will cover some basic network troubleshooting if you are having issues with any of the tasks. Teer Building 106, 10:15 am - 11:15 am.
10/9 Introduction to Unix - Unit 5: Advanced File Management
This unit will be a deeper dive into working with files and the filesystem, we will learn about linking to files elsewhere in the system, how to search for a file within the filesystem, using MD5 and SHA sums to verify file integrity, and how to search for content within files. Teer Building 106, 10:15 am - 11:15 am.
10/9 Introduction to Unix - Unit 6: Advanced Application Management
This unit will cover process management, how to see the amount of free resources on a system, and how many of these resources your jobs are using. We will cover basic job control including killing runaway processes, and also how to “background” a process so that you can log out and return to it later. Teer Building 106, 9 am - 10 am.
10/11

Introduction to Unix - Unit 7: Shell Tricks
As we start to wind down our class, our penultimate unit will cover the Bash shell, which is default for many systems, and how to edit system paths, and use tricks within the shell to ease your Unix/Linux experience, including path edits and profile tweaks. Teer Building 106, 9 am - 10 am.
10/11

Introduction to Unix - Unit 8: Grand Finale
In our final unit students will be tasked with building an application from source for their own use. This can come in quite handy if you would like to test out a new software version but find that the server you are on is not updated, we will then use what we have learned to make this application executable, and the preferred version of the application. Teer Building 106, 10:15 am - 11:15 am.
 

Career & Professional Development Offerings

Date "Science & Health Career Explorations Dinner Series"
10/18

"Science & Health Career Explorations Dinner Series: SCIENCE IN ACADEMIA: FACULTY RESEARCHERS"
Perkins 218, 6:00 pm - 7:30 pm.
11/1

"Science & Health Career Explorations Dinner Series: SCIENCE & HEALTH IN GOVERNMENT & POLICY"
Perkins 218, 6:00 pm - 7:30 pm.
11/15 "Science & Health Career Explorations Dinner Series: BIOTECH INDUSTRY: RESEARCH & BUSINESS"
Perkins 218, 6:00 pm - 7:30 pm.
11/29

"Science & Health Career Explorations Dinner Series: ALLIED HEALTH PROFESSIONALS: PHYSICIAN ASST, NURSE PRACTITIONER, GENETIC COUNSELOR"
Perkins 218, 6:00 pm - 7:30 pm.
 

Spring 2012 Genome Academy

Genome Sciences & Policy Offerings

Date "Introduction to Machine Learning and Applications in Biology"
3/20

Part I: "Introduction to Machine Learning and Applications in Biology"

This class will provide an introduction to machine learning. Instructor will define machine learning, go over common issues that must be addressed when learning from data, and cover some basic notions useful in understanding and designing machine learning algorithms. Although knowledge of statistics and probabilities is not required, basic notions of algebra will be useful. Instructor: Fantine Mordelet, PhD. Teer Building 106, 9 am - 11 am.
3/27

Part II: "Introduction to Machine Learning and Applications in Biology"

This class will more precisely focus on regression and classification problems and methods. Although knowledge of statistics and probabilities is not required, basic notions of algebra will be useful. Attendance at Part I, while not required, is suggested. Instructor: Fantine Mordelet, PhD. Teer Building 106, 9 am - 11 am.
4/3

Part III: "Introduction to Machine Learning and Applications in Biology"

This session will be dedicated to an overview of the famous "support vector machines" and, more generally, kernel methods, with examples of applications in biology. Although knowledge of statistics and probabilities is not required, basic notions of algebra will be useful. Attendance at Parts I & II, while not required, is suggested. Instructor: Fantine Mordelet, PhD. Teer Building 106, 9 am - 11 am.
4/6 Part I: "Overview of Human Subjects Protections for Genetics/Genomics Research"
Lecturer: Donna Cookmeyer, PhD, Chair, Institutional Review Board, Duke University School of Medicine
This lecture will cover the ethical foundations, federal regulations, and institutional policies governing the submission and conduct of genetic/genomic research protocols. CIEMAS 2240, 10 am - 11:30 am. Presentation Slides.
4/10

Part IV: "Introduction to Machine Learning and Applications in Biology"

Unsupervised learning refers to the problem of finding hidden structure in data. This class will give an overview of the most popular unsupervised learning techniques such as k-means clustering or Principal Component Analysis. Although knowledge of statistics and probabilities is not required, basic notions of algebra will be useful. Attendance at Parts I, II & III, while not required, is suggested. Instructor: Fantine Mordelet, PhD. Teer Building 106, 9 am - 11 am.
4/13 Part II: "Overview of Human Subjects Protections for Genetics/Genomics Research"
Lecturer: Donna Cookmeyer, PhD, Chair, Institutional Review Board, Duke University School of Medicine
Over the past several years, much debate about certain practices related to the conduct of genetics/genomics research has occurred. This lecture will discuss many of the current issues faced by genetic/genomic researchers including returning research results to subjects, obligations to disclose data-sharing practices (including those required of funding agencies), appropriate counseling/referrals, sample and DNA/RNA banking, and protection of subjects’ privacy/confidential information. Attendance at Part I of this lecture series is not required in order to attend Part II. CIEMAS 2240, 10 am - 11:30 am. Presentation Slides.
 

Career & Professional Development Offerings

Date "Science & Health Career Explorations Dinner Series"
3/20

"Science & Health Career Explorations Dinner Series: SCIENCE COMMUNICATIONS & MEDIA"
Perkins 218, 6:30 pm - 8 pm.
3/27

"Science & Health Career Explorations Dinner Series: GENETICS & DISEASE ADVOCACY ORGANIZATIONS"
Perkins 218, 6:30 pm - 8 pm.
4/10 "Science & Health Career Explorations Dinner Series: BIOTECH INDUSTRY: RESEARCH & BUSINESS"
Perkins 218, 6:30 pm - 8 pm.
4/17

"Science & Health Career Explorations Dinner Series: PHYSICIAN, PHYSICIAN/RESEARCHER: MD, MD/PhD"
Perkins 218, 6:30 pm - 8 pm.