Greater Philadelphia BioInformatics Alliance

Introduction to Molecular
Systems Biology
Mark S. Lechner, Ph.D.
Drexel University
Aleistar Saunders, Ph.D.
Drexel University

Course will focus on fundamentals of cell biology: information flow from genes to RNA to proteins, genome structure and organization, principles of regulation of genes and proteins, cells as the basic units of life, the cell division cycle, etc.

This course adopts a systems view to discuss the communication of cells with other cells and with the external environment. Particular emphasis will be given to cell division cycle because of its crucial role in development and in diseases such as cancer. Course includes a daily wet laboratory session. The wet lab sessions include aseptic/sterile cell culture techniques, cell proliferation, cell migration, NGF-induced cell differentiation and angiogenesis experiments.

Modeling in Systems Biology
Bahrad Sokhansanj, Ph.D.
Drexel University

With the advancement of quantitative measurement techniques, single molecule tracking in live cells, and large data sets available through genomics and proteomics, there is a rapidly growing need to use computers to integrate information, interpret experimental results and design new experiments, and predict the impact of gene defects and therapeutics.

This course will introduce the concept of system modeling and present a wide range of methods for simulating biological systems, discussing their potential power and pitfalls in terms of the practical needs of biological scientists. Through interactive electronic laboratories, students will work on real biological problems using a variety of computer simulation tools. Guest speakers will discuss examples of computer modeling in biological research projects and development of next-generation computational methods and tools.

Microarrays and Differential
Gene Expression
Don Baldwin, Ph.D.
University of Pennsylvania

This course will present the fundamentals of microarray experiments for high throughput measurement of RNA abundance profiles, focusing on the labwork and data analysis required to determine the probability that the genes represented on a microarray show differential expression between two or more conditions.

The course covers the initial steps necessary for analyzing the data, including experimental design, image analysis, normalization, background correction, basic statistical analysis, filtering techniques, and visualization. Tools used will include Affymetrix GeneChips, Affymetrix analysis software, and the Multi-Experiment Viewer open source application from the Institute of Genomics Research to provide hands-on experience with techniques. The course includes wet laboratory sessions conducted at the Penn Microarray Facility.

Pharmacogenomics
Kristin Ardlie, Ph.D.
Vice President of Genetics,
Genomics Collaborative, Inc.
Andres Kriete, Ph.D.
Drexel University

Pharmacogenomics is an emerging discipline focusing on the use of genome information for informed decision making along the pharmaceutical pipeline. Drug discovery has the challenging task to identify genes and gene products which are most attractive as therapeutic targets. This course reviews the bioinformatics and high-throughput methods for identification of targets, candidate drugs and their potential adverse effects, which will be exemplified further by the findings of recently conducted studies. The course presents hands on experience on computational methods used in pharmacogenomics.

Biostatistics, Clustering
and Classification
Michael Ochs, Ph.D.
Fox Chase Cancer Center

This course will introduce and define biostatistics measures used in the analysis of high throughput biological data. The microarray data analysis comprises two main parts: 1) the use of statistical methods to reliably estimate the presence of changes in mRNA levels between different conditions measured using microarrays or GeneChips and 2) the application of pattern recognition in microarray and proteomic analysis, including clustering methods and more advanced methods making use of the large body of biological knowledge for interpretation of microarray and proteomic results.

The course will include hands-on data analysis using TMEV open source tool from The Institute for Genomics Research (TIGR), Oak Ridge National Laboratory’s GO Tree Machine (GOTM) gene ontology tool, and ClutrFree open source visualization tool from Fox Chase Cancer Center.

Bioinformatics Databases
and Biomolecular Networks
Greg Gonye, Ph.D.
Thomas Jefferson University
Michael Ochs, Ph.D.
Fox Chase Cancer Center

This short course will focus on computational data resources and approaches which allow expanding from single gene analyses to system-level analyses. In particular integrative databases which combine diverse data classes, from genome sequence to gene expression to functional ontology classification will be showcased. Tools which build on these resources to predict regulatory, functional and/or “knowledge” network interactions will be used to analyze the data produced in the previous weeks.

A focus on hands-on tutorials using real data should provide participants with a good working knowledge of these valuable systems biology resources.

Integrative Biology Research
in Philadelphia
Discussion Leaders - TBA
Computational Genomics, Protein
Modeling, Translational Medicine, Integrative Cancer Biology

Each day of this four-day session will form around the on-going regional research for the listed topics. Participants are welcome to attend, free of charge, to listen, contribute their ideas, and discuss collaborative opportunities in these fields.

Proteomics
David Speicher, Ph.D.
The Wistar Institute
Hsin-Yao Tang, Ph.D.
The Wistar Institute
Nadeem Ali-Khan, Ph.D.
The Wistar Institute
Peter I. Lelkes, Ph.D.
Drexel University

Proteomics, the systematic analysis of proteins in cellular machines, entire cells, tissues or entire organisms, represents an exciting new way to pursue biological and biomedical science in taking a comprehensive, systematic approach to understanding biology.

This course will provide an in-depth examination of the types of problems that proteomics can address, the alternative tools that are available, and how to match biological problems to available analytical tools. A major focus will be the central role of mass spectrometry in proteomics and the computational challenges associated with analysis and interpretation of diverse types of proteomic data. Lectures will be interspersed with hands-on data analysis tutorials and lab demonstrations.

PAST EVENTS

Virtual Institute

Seminar Series

Computational Orchestra

Research @ GPBA Member Labs

Virtual Institute – Summer Session 2005

Director: Aydin Tozeren, Ph.D., Drexel University

http://www.gpba-bio.com/vi_2005.asp

Frequently Asked Questions

What is the Summer Session course schedule?

June 6 – June 10		Microarrays and Differential Gene Expression
June 13 – June 17		Pharmacogenomics
June 20 – June 24		Biostatistics, Clustering, and Classification
June 27 – July 1		Bioinformatics Databases and Biomolecular Networks
July 5 – July 8 *		Integrative Biology Research in Philadelphia
July 11 – July 15		Proteomics

* this week will be open and free of charge to all participants

Who will teach the Summer Session courses?

A tentative list of course instructors follows:

Kristen Ardlie, Ph.D., Vice-President of Genetics, Genomics Collaborative
Don Baldwin, Ph.D., University of Pennsylvania
Greg Gonye, Ph.D., Thomas Jefferson University
Andres Kriete, Ph.D., Drexel University and Coriell Institute for Medical Research
Mark Lechner, Ph.D., Drexel University
Michael Ochs, Ph.D., Fox Chase Cancer Center
Aleister Saunders, Ph.D, Drexel University
Bahrad Sokhansanj, Ph.D., Drexel University
David Speicher, Ph.D., Wistar Institute

In addition to this excellent cadre of instructors, GPBA is currently forming commitments from prominent academic and industry scientists to guest lecture during the Summer Session.

How much do the Summer Session courses cost?

Tuition costs breakdown as follows:

	Single Course Price	Multiple Course Price ($/course)
Industry Professionals/ Post-Docs/ Fellows	$950	$800
Graduate/Undergrad Students*	$750 (for non-GPBA or non-credit students) Tuition (for students taking classes for credit at GPBA member institutions)

* One week of coursework is equivalent to 1 semester credit hour. Students from GPBA affiliated universities (including Children’s Hospital of Philadelphia, Drexel University, Penn State Great Valley, Temple University, Thomas Jefferson University, University of Pennsylvania, and University of the Sciences in Philadelphia) may sign up for credits at their individual institutions through their GPBA Executive Committee members. All students must also register through the GPBA website to be included in the roster and ensure a seat in the course.

When and where will the courses be held?

The first week begins on Monday June 6, 2005. The courses are held on Monday through Friday from 12:30pm – 6:00pm with the exception of Introduction to Molecular Systems Biology which consists of lecture from 10:00am – 12:00pm and wetlab from 1:00pm – 6:00pm. Each subsequent week begins on the following Monday. Courses will be held primarily in the new Edmund D. Bossone Research Enterprise Center (32nd and Market Streets) on the campus of Drexel University, Philadelphia, PA. Microarray and Proteomics lab sessions will be held at the Penn Microarray Facility (3620 Hamilton Walk), University of Pennsylvania, and the Proteomics Lab ( 3601 Spruce Street), The Wistar Institute, respectively. Locations including facility details and room numbers will be distributed upon confirmation of registration in the program.

What important dates do I need to remember for application and registration?

The application and registration process will follow this sequence around the dates indicated below:

Open Application – March 17th

Application Deadline – May 15th

Courses Begin - June 6th

Can I get credit from my institution? How?

Undergraduate and graduate-level students are eligible for one semester-hour of credit for each week attended. Students from GPBA affiliated universities may sign up for credits at their individual institutions through their GPBA Executive Committee members.

The Children's Hospital of Philadelphia Dr. Peter White white@genome.chop.edu	Drexel University Dr. Aydin Tozeren tozeren@coe.drexel.edu
Penn State Great Valley Dr. David Russell drussell@psu.edu	Temple University Dr. Zoran Obradovic zoran.obradovic@temple.edu
Thomas Jefferson University Dr. Greg Gonye ggonye@mail.dbi.tju.edu	University of Pennsylvania Dr. Susan Davidson susan@cis.upenn.edu
University of the Sciences in Philadelphia Dr. Randy Zauhar r.zauhar@usip.edu

Are hotel accommodations provided?

No, however, accommodations in student housing within walking distance and/or convenient public transportation may be reserved for a modest fee by contacting:

Dr. Aydin Tozeren
Drexel University
(215) 895-6148
Tozeren@cbis.ece.drexel.edu

If you prefer hotel accommodation, hotels within a short walk of the course facilities are:

Sheraton University City Hotel
3549 Chestnut St
Philadelphia
Pennsylvania 19104
Tel: +1 215 387 8000
Fax: +1 215 387 7920
http://www.philadelphiasheraton.com/

The Inn at Penn, A Hilton Hotel
3600 Sansom Street
Philadelphia, PA 10104
Tel: +1 215 222 0200
Fax: +1 215 222 4600
http://www.theinnatpenn.com/index.asp

International House
3701 Chestnut Street
Philadelphia , PA 19104
Tel: +1 215 387 5125
http://www.ihousephilly.org

The Divine Tracy Hotel
20 South 36th Street
Philadelphia, PA. 19104
Tel: +1 215 382 4310
Fax: +1 215 387 0157
E-mail: divent9@verizon.net

The Greater Philadelphia Bioinformatics Alliance reserves the right to change information in this FAQ and on the Virtual Institute web page. Please stay informed by checking the website periodically for updates.

This project was financed, in part, by a grant from the Commonwealth of Pennsylvania, Department of Community and Economic Development.