Biomedical Informatics Short Courses 2010
Title: A Short Course in Genomics: Microarrays and High Throughput Sequencing
Application form (see instructions below)
Dates: May 10 -14, 2010
Location: University of the Western Cape
Instructors: Gavin Sherlock, PhD, Assistant Professor, Department of Genetics, Stanford School of Medicine, Catherine Ball, PhD, Director, Stanford Microarray Database, Department of Biochemistry, Stanford School of Medicine, Curtis Huttenhower, PhD, Assistant Professor, Dept. of Biostatistics, Harvard School of Public Health.
The last decade has seen an explosion in high-throughput technologies, making it relatively straightforward to generate biomedical datasets of millions, or even billions of data points in a short time. Such datasets provide a significant challenge for their analysis, requiring researchers to often spend more time analyzing data than generating it. Since large-scale datasets will become larger and more common in the future, it is thus essential for biomedical researchers today to possess the skills to manipulate and analyze them. To enable students to analyze and understand their own data, this fast-paced tutorial will provide hands-on experience that complement lectures with analysis exercises as well as discussion sections exploring relevant recent publications. For microarray data analysis, we will cover normalization, hierarchical clustering, k-means clustering, bi-clustering, GO analysis and Gene Set Enrichment Analysis, as well as identification of genes with significant changes in expression. For high-throughput sequencing applications, we will cover tools and techniques for read mapping, analysis of RNA-Seq and ChIP-Seq data, assembly of short reads into contigs, SNP analysis, as well as emerging file formats.
Call for Participation
Students in the Stanford-South Africa Biomedical Informatics (SSABMI) program are expected to participate in the short course.
Students, faculty, staff from other educational institutions in South Africa with interest in biomedical informatics may apply for any of these short courses by enrolling through SANBI or by contacting the SSABMI program directly. Space is limited. Priority is given to those who are involved in or who wish to develop research programs in biomedical informatics. (You may wish to read our definition of biomedical informatics).
About fees and funding
We do not charge registration fees for the course.
We regret that our funds cannot support travel or lodgings to the University of the Western Cape or Cape Town.
About the location: University of the Western Cape, room location - TBA
Instructions for applications: Download the application form, complete the forms and email to 
Deadline to submit applications: April 21, 2010
Dr. Adele Kruger
Programme Coordinator
Stanford-South Africa Biomedical Informatics Programme
Private Bag X17
University of the Western Cape, SANBI
Bellville, 7535
Republic of South Africa
adele <_AT_> sanbi.ac.za (the <_AT_> stands for the @ symbol)
tel: +27 (0) 21 959 3910
Fax: +27 (0) 21 959 2512
Biomedical Informatics Short Courses 2007
Short courses are coordinated with established bioinformatics courses at the University of the Western Cape (UWC), and are taught by world-class faculty from Stanford University, the University of Western Cape, the University of Cape Town, and the South African National Bioinformatics Institute (SANBI). Each course will utilize didactic lectures, demonstrations, research presentations, group discussions, and interactive exercises to teach key concepts and applications. Typically classes are 3-5 days in duration.
New and continuing students in the Stanford-South Africa Biomedical Informatics (SSABMI) program are expected to participate in the short course offered Dec. 3-6, 2007.
Students, faculty, staff from other educational institutions in South Africa with interest in biomedical informatics may apply for any of these short courses by enrolling through SANBI or by contacting the SSABMI program directly. Space is limited. Priority is given to those who are involved in or who wish to develop research programs in biomedical informatics. (You may wish to read our definition of biomedical informatics).
If you cannot attend our short courses, we videotape some of our short courses. At the present time, we have DVD's of our Pharmacogenomics class. More information
Intermediate Statistics for Biomedical Research
Instructor: Michael G. Walker, Associate Consulting Professor, Stanford Medical Informatics
Dates: Dec. 3-6, 2007
Location: University of the Western Cape, Belleville (Cape Town), South Africa
This intermediate-level course will cover the statistical methods most frequently used in biomedical research, and guide students to perform their own analyses using Excel and the R statistics software. The first day of lectures will review statistical methods covered in an introductory course, including descriptive statistics, probability, t-tests, and analysis of
variance. Subsequent lectures will cover multivariate analysis of variance, non-parametric methods, categorical data analysis, multivariate regression, survival analysis, sample size and power calculations, and corrections for multiple testing. The emphasis of the course is on practical applications and understanding concepts, rather than on formulas or proofs. Students will perform example analyses using Excel and R.
Instructions for AppLication
The short course will be held Dec. 3-6, 2007. We recommend students enter the class with "Introduction to Biomedical Statistics" or equivalent (see below for course description). However, the first day of the class will be spent reviewing introductory concepts. The deadline for submission of applications is Oct. 17, 2007.
Prerequisite for Intermediate Biomedical Statistics
Introduction to Biomedical Statistics
The Introduction to Biomedical Statistics course provides a practical introduction to the statistical methods that are most commonly used in biomedical research. Emphasis will be on when and how to use the methods rather than on proofs. Students will learn how to describe data and detect unusual values, compare treatment effects, interpret p-values, detect and quantify trends, detect and measure association and correlation, determine the sample size and power for an experiment, and choose appropriate statistical tests and software. Examples will include use of statistical analysis software, and will focus on bioinformatics applications including gene expression analysis.
Did you miss some of our previous short courses?
You can still view the lectures on DVD. We have captured the Pharmacogenomics short course electronically. If you are an educational program in South Africa or if your program is funded by the Fogarty International Center (a division of the National Institutes of Health), we will send you a set for free.
If your educational program is not located in South Africa or funded by the Fogarty, you can still obtain the DVD's but we request a shipping and handling fee.
PHARMACOGENOMICS AND PHARMACOGENETICS ON DVD
Russ B. Altman, MD, PhD, Professor of Genetics, Medicine and by courtesy Computer Science, Stanford University and Caroline Thorn, PharmGKB, Scientific Curator.
The Pharmacogenomics course introduces students to informatics applications in the area, with a special focus on the PharmGKB database, a publicly available internet research tool developed by Stanford University to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs.
Course topics include:
- Drug response
- Ways to measure phenotypes
- Clinical examples
- Single Nucleotide Polymorphism analyses and associated genotype/phenotype
Biomedical Informatics Short Courses 2006 - Now CompleteD!
2006 SSABMI Short Course
Database Design and Database Mining:How to Manage and Learn from Biological and Medical Data
Instructors: Amar Das, MD, PhD, Asst. Prof., Stanford Biomedical Informatics Training Program, Stanford Medical Informatics, Martin O'Connor, MSc, Software Engineer, Stanford Medical Informatics.
Sept. 5-7, 2006
Optional Sessions: Sept. 4 and 8, 2006
University of the Western Cape, Cape Town,
old Science Building
Z29 Computer Lab
In studying human diseases and their treatments, health care and biomedical researchers often need to deal with large amounts of data and to identify critical relationships among them. Any endeavor that needs to maintain, integrate and share information requires database software. The relational data model, developed three decades ago, is now the most widely used approach for implementing commercial database management systems. Relational database management systems have been successfully used as the infrastructure of large-scale bioinformatics and clinical outcome projects. Once properly designed and maintained, a database system can be a ‘gold mine’ for ongoing data analysis and data mining.
Through a combination of lectures and in-class computer exercises, using freely-available software and case studies, the Database Design and Database Mining course will provide a hands-on introduction to the design, implementation, and management of relational databases and to the querying and mining of relational data for health care and biomedical endeavors.
Course topics include how to:
- Represent complex data (such as patient outcomes, experimental observations, and public health studies) effectively in databases
- Understand the relational model
- Identify entities and relationships among data
- Ensure data integrity
- Implement and populate a MySQL database
- Retrieve data through the SQL query language
- Build a knowledge source using a database management system
- Use knowledge discovery methods with databases
- Extract data for mining (such as in Weka)
- Deal with heterogeneity among existing data
- Create useful database applications
The optional, introductory session will be held on Sept. 4th. This session will introduce basic operations on the computer, i.e., browsers, search engines and file formats; installation of software, e.g., MySQL and WEKA; and finally conversion of data from different formats into a form suitable for MySQL. If you have your own data set or research problem and desire a individual consultation about setting up a database and datamining, please sign up for this session.
Sept. 8, is reserved for special consultations with Martin O'Connor, who has considerable expertise on designing software architectures with database backends, which will not be covered in depth during the short course. These sessions are by appointment only. If you would like an appointment, please describe the nature of your problem in your application and indicate that you would like to schedule an appointment on the 8th.
The short course sessions will combine lectures and in-class computer exercises and will be held from Sept. 5th-7th from 9 AM - 4PM (approximately). There will be morning, lunch and afternoon breaks.
Prerequisites: Basic computer literacy. Applicants who are not comfortable with the use of routine applications on the PC, such as, Word, Excel, Internet Explorer, internet searches, program downloads, extraction and installation of packages such as MySQL and WEKA should attend the introductory session on Sept. 4. In addition, applicants should have some training or background in health care or biomedical field. Attendees are encouraged to bring examples of their own biomedical data sets for their use in hands-on tutorials.
Biomedical Informatics Short Courses 2005 - Now CompleteD!
Students accepted into the Stanford-South Africa Training Program will participate in a series of one to three-week long short courses held in South Africa, and organized into 4 modules:
- Introduction to Bioinformatics Oct. 14
- HIV and TB for Informatics (HIV: Part I) Sept 12-15
- The HIV Drug Resistance Database (HIV: Part II) Sept 16, 19-22
- Pharmacogenomics and Pharmacogenetics Oct. 17-20
- Statistics for Biomedical Research Sept. 5-8
- Ontology Engineering with Protégé Oct. 3-6
- Click on the title of past courses for the class photos!
Short courses are coordinated with established bioinformatics courses at UWC, and are taught by world-class faculty from Stanford University, the University of Western Cape, the University of Cape Town, and the National Bioinformatics Network. Each course will utilize didactic lectures, demonstrations, research presentations, group discussions, and interactive exercises to teach key concepts and applications.
Students, faculty, staff from other educational institutions in South Africa with interest in biomedical informatics may apply for any of these short courses by enrolling through the National Bioinformatics Network or by contacting the SSABMI program directly. Space is limited. Priority is given to those who are involved in or who wish to develop research programs in biomedical informatics.
INTRODUCTION TO BIOINFORMATICS
Russ B. Altman, MD, PhD, Professor, Genetics and Medicine (and, by courtesy, Computer Science), Stanford University
Oct. 14, 2005
A general introduction to the field of bioinformatics. Topics include historical context, implications of bioinformatics on biology and computer science, scope and breadth of the field and future directions.
HIV AND TB FOR INFORMATICS
David Katzenstein, MD, Professor, Infectious Diseases and Global Medicine, Stanford University
September 12-15, 2005
This course is an introduction to the biology of HIV/TB for informatics students. It will be taught by Dr. David Katzenstein (Stanford University), with talks by Dr. Robert Shafer (Stanford University), Dr. Carolyn Williamson (University of Cape Town), and Dr. Lynn Morris (National Institute for Communicable Diseases).
The course introduces students to biomedical informatics applications to the global AIDS pandemic and the HIV/AIDS and TB epidemics in South Africa, with in-depth lectures on the following topics:
HIV DRUG RESISTANCE DATABASE
Robert Shafer, MD, Asst. Professor, Infectious Diseases, Stanford University and Tulio de Oliveira, Marie Curie Fellow, Department of Zoology, Oxford University.
Please note the corrected dates below:
September 16, 19-22 2005
Students will learn how to develop HIV/TB drug databases as an informatics tool to monitor international drug resistance, and will utilize the Stanford HIV Drug Database as a learning tool throughout the course.
PHARMACOGENOMICS AND PHARMACOGENETICS (You can still view this class on DVD!)
Russ B. Altman, MD, PhD, Professor of Genetics, Medicine and by courtesy Computer Science, Stanford University and Caroline Thorn, PharmGKB, Scientific Curator.
October 17-20, 2005
The Pharmacogenomics course introduces students to informatics applications in the area, with a special focus on the PharmGKB database, a publicly available internet research tool developed by Stanford University to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs.
Course topics include:
We have captured the Pharmacogenomics short course electronically. If you are an educational program in South Africa or if your program is funded by the Fogarty International Center (a division of the National Institutes of Health), we will send you a set for free.
If your educational program is not located in South Africa or funded by the Fogarty, you can still obtain the DVD's but we request a shipping and handling fee.
More information about Biomedical Informatics Curriculum Development & DVD order instructions
STATISTICS FOR BIOMEDICAL RESEARCH
Michael G. Walker, PhD, Consulting Asst. Professor, Stanford Medical Informatics, Stanford University.
September 5-8, 2005
The Biomedical Probability and Statistics course provides a practical introduction to the statistical methods that are most commonly used in biomedical research. Emphasis will be on when and how to use the methods rather than on proofs. Students will learn how to describe data and detect unusual values, compare treatment effects, interpret p-values, detect and quantify trends, detect and measure association and correlation, determine the sample size and power for an experiment, and choose appropriate statistical tests and software. Examples will include use of statistical analysis software, and will focus on bioinformatics applications including gene expression analysis.
ONTOLOGY ENGINEERING WITH PROTÉGÉ
Samson Tu, Senior Research Scientist and Ray Fergerson, Senior Research Scientist, PROTÉGÉ Team, Stanford Medical Informatics, Stanford University
October 3-6, 2005
How do humans reason? We create mental models of the problem using concepts that are expressed mathematically as symbols and figures or as spoken and written languages such as English. Before we can expect to automate any human problem-solving process, we must express the problem in terms that the computer can manipulate and which the human community can understand. We create a model of our body of expertise (biomedical concepts), known as the knowledge representation and duplicate our reasoning processes on this body of knowledge using algorithms (simulation, probabilistic reasoning, artificial intelligence, machine learning, etc...) in order to produce software that automates one of our problem-solving procedures. This process lies at the heart of every reasoning task which has been automated.
An ontology or knowledge representation is a formal "specification of a conceptualization" . As a simple example of an ontology, we may visualize a cell as a collection of macromolecules (proteins, lipids, nucleic acids, etc...). Therefore, providing the name, location in space and chemical identity of all macromolecules should be sufficient to specify our simple conceptualization of a cell. The development of an appropriate ontology/knowledge representation has historically been an integral part of the software development process. As our body of knowledge grows in depth and complexity, it becomes difficult for one team of software engineers/biomedical domain experts to maintain the knowledge representation to keep current software implementations running. Developing new reasoning tasks becomes a formidable challenge. We need to develop methods where we can maintain and extend biomedical ontologies as a community rather than as individual informaticians.
The Ontology Development With Protégé course provides a hands-on introduction to the field of ontology engineering and knowledge-base development using Protégé. Protégé is a freely-available software platform which supports manual development of ontologies. It includes features which support community development of ontologies, consistency checking, support for multiple data representations, etc...
Course topics include:
This work supported by the NIH/Fogarty International Center under grant D43 TW00699