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 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
Genome Academy Spring 2007
Introductory PERL Classes
3/27, 3/29, 4/3, 4/5, 4/10 and 4/12
10am - 11am
Duke Bostock Library Computer Room, 023
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. The courses will be held over three weeks on 3/27, 3/29, 4/3, 4/5, 4/10 and 4/12 from 10am - 11am in the Duke Bostock Library Computer Room, 023. Please see the course webpage, for additional information. Seating is limited, so please reserve your spot by contacting Jennifer Avery.
Genome Academy Fall 2006
Genomes 101: Introductions to the Genome Sciences
Tuesdays from 4:00pm to 5:00pm
Medical Student Amphitheater, Duke South Room 0916 (located in the basement across from the cafeteria)
Free, registration encouraged.
Access streaming video of past lectures
| Date | Title | Speaker |
| 10/3 | Introduction to Genome Sciences *session for this date only will run from 4:00pm - 5:15pm and will be held in Bryan Research Building, Room 103 | Hunt Willard, Director, IGSP |
| 10/10 | Sequencing and Sequence Analysis Presentation Slides Dideoxy Sequencing |
Fred Dietrich, IGSP; Dept. Molecular Genetics & Microbiology |
| 10/17 | Genome Browsers and Databases Presentation Slides I Presentation Slides II Presentation Slides III |
Jamie Cuticchia, Director, Duke Bioinformatics Group; IGSP, CCC |
| 10/24 | Microarrays and Molecular Profiling Presentation Slides |
Holly Dressman, Director, IGSP Microarray Facility |
| 10/31 | Genotyping Technologies Presentation Slides |
Kevin Shianna, Director, IGSP Genotyping Facility |
| 11/7 | Ethical & Policy Issues in Research Involving Human Biospecimens *session for this date only will be held in the Alban K. Barrus Classroom, room 3031 in Duke South Presentation Slides |
Laura Beskow, Associate Director, Research Ethics, IGSP Center for Genome Ethics, Law & Policy |
| 11/14 | Population Genetics | David Goldstein, Director, IGSP Center for Population Genomics & Pharmacogenetics |
| 11/21 | Clinical Research Applications: Cancer Genomics Presentation Slides |
Phil Febbo, IGSP: Dept. Medicine - Oncology |
Limited Space Available. Please Email Jennifer Avery to register.
Past Course Offerings:
Genomes 101: Introductions to the Genome Sciences
Focused presentations on the current study of genome sciences; enabling researchers to make the most of available genome technologies. Ten (10) 1-hour sessions
PERL: A Brief Introduction
PERL is arguably the most used language in the field of bioinformatics. Learn how to begin using this Practical Extraction and Reporting Language in your day to day research tasks. Five (5) 1-hour sessions. Instructor: Darin London.
Introduction to Database Design using MySQL
Over the course of six one hour sessions, this class will introduce the concepts of relational databases and practical ways to use them. Topics will include: when (and when not to) consider using relational databases; how do properly design database schemas; and how to interact with databases using SQL. The course will focus largely on proper database design principles using a simple bioinformatics related schema as a model. Participants are encouraged to attend every class as new material will build on previous sessions. Instructor: Rob Wagner.