Genome Academy
Advances in genome sciences and the approaches used to study them have developed at an incredible pace. The Genome Academy is intended to help researches at all levels gain the background to begin or enhance their own genomics research projects through various topical learning series. The offerings will vary each year to reflect novel technologies as well as demand. Please see the schedule below for current and past offerings. Each series is offered free of charge to the Duke Community. Register early as some series may fill up quickly. For more information or to register, contact Shandra Robertson 684-3156.
Genome Academy Fall 2009
Genomes 101: Introductions to the Genome Technologies and Applications. Focused presentations on the current technological resources available and its research applications. You can download the PowerPoint slides from past presentations by clicking on the title of the talk. The audio for each lecture is located at iTunes U.
Wednesdays from 4:00 p.m. to 5:00 p.m.
Bryan Research Building Room 103
| Date | Title | Speaker |
| 9/9 | Genome Browsers and Databases | Terry Furey, IGSP; Biostatistics and Bionformatics |
| 9/23 | Sequencing and Sequence Technologies | Fred Dietrich, IGSP; Dept. of Molecular Genetics and Microbiology |
| 9/30 | Genotyping/Next Generation Sequencing | Kevin Shianna, Director, IGSP Genotyping Facility |
| 10/7 | RNAi Technology | James Pearson, Manager, RNAi Facility |
| 10/21 | Proteomics | Arthur Moseley, Director, Duke Proteomics Core Facility |
| 11/11 | Personalized Medicine | Alex Cho, Dept. Medicine – General Internal Medicine |
| 11/18 | Clinical Research Applications | Phil Febbo, IGSP; Dept. Medicine - Oncology |
For more information contact Shandra Robertson at 684-3156, or shandra.robertson@duke.edu.
Genome Academy Spring 2009
Genome Academy is intended to help researches at all levels gain the background to begin or enhance their own genomics research projects through various topical learning series. Each series is offered free of charge to the Duke Community.
Topics include:
- Intermediate Unix
- Data Mining in Qualitative and Quantitative Proteomic Data Sets
- Keeping Up: The Art of Discovering What's New in Research
- Next-Generation Sequencing Technologies and Applications
- Introduction to Oracle
| Date | Topic | Speaker |
| 1/28 | Intermediate Unix 10:00am - 12:00pm Bostock Computer Lab, Room 023 |
Peyton Vaughn Systems Administrator |
| 2/4 | Data Mining in Qualitative and Quantitative Proteomic Data Sets 1:00om - 2:00pm Nanaline Duke Auditorium, Room 147 |
Arthur Moseley, PhD Director, Proteomics Core Facility |
| 2/18 | Keeping Up: The Art of Discovering What's New in Research 1:00pm - 2:00pm Bostock Computer Lab, Room 023 |
Andrea Novicki, PhD, Center for Instructional Technology Darin London, Senior IT Analyst, IGSP Teddy Gray, Biological and Environmental Sciences Librarian |
| 3/18 | Next-Generation Sequencing Technologies and Applications 1:00pm - 3:00pm Nanaline Duke Auditorium, Room 147 |
Greg Wray, PhD, Director, Center for Evolutionary Genomics Lisa Bukovnik, Manager, DNA Sequencing Facility |
| 4/1 | Introduction to Oracle 9:00am - 12:00pm Bostock Computer Lab, Room 023 |
Rob Wagner Senior Database Administrator, IGSP |
Class Descriptions
This course will build off of the fundamentals covered in the introductory course, with a continued intent of increasing exposure to basic tools available to the Unix user. The goal of this course is to enable researchers to integrate Unix into their workflow. Topics to be covered include: shell configuration; file access; process control; basic shell scripting. The class will consist of one (1) 2-hour session.
Instructor: Peyton Vaughn.
Wednesday, January 28, 2009
10:00 a.m. - 12:00 p.m.
Bostock Library Computer Lab—Room 023
Data Mining in Qualitative and Quantitative Proteomic Data Sets
Description: The goal of this seminar is to help IGSP scientists better understand the nature of the data contained in LC/MS/MS proteomics datasets, and introduce them to the tools available for mining of these datasets. This seminar will address data mining using three principal software tools - Mascot (Matrix Sciences), Scaffold (Proteome Software), and Elucidator (Rosetta). In our IGSP Proteomics Core, we use Mascot and Scaffold primarily as tools for mining qualitative proteomic datasets, whereas Elucidator is used for mining of datasets containing both qualitative and quantitative information. The utility of these tools will be illustrated using data from two studies - a cancer cell line experiment looking at drug treatment and drug resistance phenotypes, and a clinical dataset looking for serum biomarkers predictive of treatment response in chronic HCV infection.
Students are strongly encouraged to visit the websites of the vendors of these three software tools prior to attending the seminar, as each contains useful tutorials on the software. In particular, the Scaffold and Mascot websites have an extensive set of reference materials, as well as specifics on the use of their software packages.
Mascot
- website
- reference page
Scaffold
- website
- tutorials
- "Proteomics for Pedestrians"
Elucidator
- website
Instructor: Arthur Moseley PhD, Director, Proteomics Core Facility
Wednesday, February 4, 2009
1:00 p.m. - 2:00 p.m.
Nanaline Duke Auditorium, Room 147
Keeping Up: The Art of Discovering What's New in Research
Keep up with your research interests quickly and easily from your own computer by focusing on a new, non-email based internet technology. This new feature is designed to notify you as new information develops. If you read blogs or track stories on your favorite news website, you have already used this technology but you may not know how powerful it is or what it can do to revolutionize the way you track the things that interest you. If you still rely on email to notify you of new developments, you should also attend to break away from the ever-growing junk mail that plagues your system. Come find out just how powerful and easy it is to use this system and how IGSP-IT is already making use of it in many of the webservices that we have developed. The class will consist of one (1) 1-hour session.
Instructors: Mark DeLong, PhD, Andrea Novicki, PhD, Darin London, and Teddy Gray..
Wednesday, February 18, 2009
1:00 p.m. - 2:00 p.m.
Bostock Library Computer Lab—Room 023
Next-Generation Sequencing Technologies and Applications
Come hear an overview of the Next-Generation sequencing technologies currently available at the IGSP Sequencing Facility. Applications will be discussed, with special attention given to work contracted in the Facility by Duke researchers. Practical questions about sample preparation, cost, and bio-informatics issues will also be addressed. We will end the session by briefly discussing single-molecule sequencing, which is next on the technological horizon.
Instructor: Greg Wray
Wednesday, March 18, 2009
1:00pm - 3:00pm
Nanaline Duke Auditorium, Room 147
Introduction to Oracle
This course will provide a quick introduction to relational databases and illustrate their utility in the genome sciences. Basic relational database concepts, such as schemas, tables, and relationships, will be discussed. The focus of the course, however, will be on teaching skills for querying single and multiple tables and manipulating data in an existing database using Oracle SQL. Because of time constraints, schema design will not be covered. Participants should be comfortable using the Linux command line prior to taking this course. The class will consist of one (1) 3-hour session.
Instructor: Robert Wagner
Wednesday, April 1, 2009
9:00 a.m. - 12:00 p.m.
Bostock Library Computer Lab—Room 023
Genome Academy Fall 2008
Focused lectures on the current systems, languages, and tools used in bioinformatics, enabling researchers to make the most of available programming fundamentals within their home disciplines.
Topics include:
Registration is required and seating is limited. For more information or to register, contact Shandra Robertson 684-3156.
Schedule for Fall 2008
Tuesdays and Thursdays @ 11am-12p.m. • Bostock Computer Lab, Room 023
* October 23rd class to be held October 24th
| Date | Topic | Speaker |
| 10/7 | Introduction to Unix | Peyton Vaughn IGSP; Systems Administrator |
| 10/9 | PERL II: Parsing, Packing, Objects, and BioPerl—Session 1 of 6 |
Darin London IGSP, Senior Systems Analyst |
| 10/14 | PERL II—Session 2 of 6 | Darin London IGSP, Senior Systems Analyst |
| 10/16 | PERL II—Session 3 of 6 | Darin London IGSP, Senior Systems Analyst |
| 10/21 | PERL II—Session 4 of 6 | Darin London IGSP, Senior Systems Analyst |
| 10/24 | PERL II—Session 5 of 6 | Darin London IGSP, Senior Systems Analyst |
| 10/28 | PERL II—Session 6 of 6 | Darin London IGSP, Senior Systems Analyst |
| 11/05 | Introduction to Unix | Peyton Vaughn IGSP; Systems Administrator |
| 11/12 | Introduction to the Sun Grid Engine | John Pormann Director, Information Technology, BME VPIT-Research Computing |
Class Descriptions
This course presents a broad overview of Unix concepts and tools. The intent is to help the user become comfortable working in a Unix environment. Familiarity with Unix is important for those who want to use computational tools for genomic investigations. Covered topics will include: understanding the shell environment; using a text editor; working with files; useful commands; compiling software. The class will consist of one (1) 2-hour session.
Instructor: Peyton Vaughn.
Tuesday, October 7, 2008
10:00 a.m. - 12:00 p.m.
Bostock Library Computer Lab—Room 023
Wednesday, November 5, 2008
1:00pm - 3:00pm
Bostock Library Computer Lab—Room 023
PERL II: Parsing, Packages, Objects, and BioPerl
PERL is arguably the most used language in the field of bioinformatics. Learn how to parse a given text file of complex biological data in ways that facilitate further computational analysis. Class will finish with a 2-day mini lab which introduces and uses some of the packages that are included in the widely popular BioPerl modules. The class will consist of six (6) 1-hour sessions. Intro to PERL course or previous experience with basic PERL programming recommended.
Instructor: Darin London.
Syllabus
Tuesdays and Thursdays @ 11:00 a.m. - 12:00 p.m.
Bostock Library Computer Lab—Room 023
October 9th through October 28th
*October 23rd class to be held October 24th
Introduction to Sun Grid Engine
This seminar will introduce the Sun Grid Engine batch scheduling system. SGE is used on the Duke Shared Cluster Resource to fairly share computational resources among many users. This seminar will describe how to use SGE to submit and track jobs, as well as cover some basic aspects of shell scripting. The class will consist of one (1) 1-hour session.
Instructor: John Pormann
Wednesday, November 12, 2008
11:00 a.m. - 12:00 p.m.
Bostock Library Computer Lab—Room 023
Previous Years
Genome Academy Spring 2008
Introduction to Perl
Register today for a series of Perl classes, offered as part of the IGSP Genome Academy. These introductory-level courses will cover Perl syntax, sample programs and more. They will be held over three weeks on 4/7, 4/9, 4/14, 4/16, 4/21 and 4/23 from 1-2pm in the Duke Bostock Library Computer Room, 023. Please see the course webpage, http://perlsoflondon.pbwiki.com/Syllabus, for additional information.
Seating is limited, so please reserve your spot by contacting Jennifer Avery at jennifer.avery@duke.edu.
Genome Academy Fall 2007
Perl: Level II
Register today for a series of advanced Perl classes, offered as part of the IGSP Genome Academy. These courses are designed to introduce the use of Perl as a parsing language, using real-world datasets as examples.
Anyone with a basic knowledge of Perl (e.g. having taken the Genome Academy Perl I class, or read a Perl book and written a few scripts of their own) may enroll. Duke faculty, staff or students may attend at no charge.
The courses will be held over three weeks on 10/22, 10/24, 10/29, 10/31,
11/5 and 11/7 from 11am – noon in the Duke Bostock Library Computer Room, 023.
Seating is limited, so please reserve your spot by contacting Jennifer Avery at jennifer.avery@duke.edu. Also, in order to make the class more pertinent, attendees are invited to submit datasets to be used as examples in the class. Please bring any datasets that you would like to be considered to the first class session on 10/22.
Genomes 101: Introductions to the Study of Genome Sciences
This course presents a broad overview of genome sciences research. Each session is devoted to a unique facet of genome research from bench to clinical research applications. This course is intended as an introduction for Duke researchers including faculty, students, technicians, residents and fellows.
Tuesdays from 4:00pm to 5:00pm
103 Bryan Research Building
Free, registration encouraged.
| Date | Title | Speaker |
| 9/18 | Sequencing and Sequence Analysis | Fred Dietrich, IGSP; Dept. Molecular Genetics & Microbiology |
| 9/25 | Genome Browsers & Databases | Jamie Cuticchia, Director, Duke Bioinformatics Group; IGSP, CCC |
| 10/2 | RNAi Technology | Mariano Garcia-Blanco, Dept. Molecular Genetics & Microbiology |
| 10/9 | Microarrays and Molecular Profiling | Holly Dressman, Director, IGSP Microarray Facility |
| 10/16 | Genotyping Technologies | Kevin Shianna, Director, IGSP Genotyping Facility |
| 10/23 | Proteomics | Art Moseley, Director of Duke Proteomics Core Facility |
| 10/30 | Complex Disease Genetics | Jeanette McCarthy, IGSP, Dept. of Community and Family Medicine |
| 11/6 | Cancer Genomics | Phil Febbo, IGSP, Depts. of Medicine & Oncology |
| 11/13 | Ethical & Legal Issues in Genomic Research | Lauren Dame, Associate Director, IGSP Center for Genome Ethics, Law & Policy |
Access streaming video of the Genome Academy lectures:
http://lectopia.oit.duke.edu/lectopia/lectopia.lasso?ut=291