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The Bioinformatics Core hosts workshops of relevance to scientists in the Penn community on topics related to bioinformatics. If you would like to suggest a topic, please send email to workshops@pcbi.upenn.edu and we will consider adding your topic to the schedule.
Upcoming workshops:
Past workshops
Most workshops are offered twice a year, and sessions are usually scheduled 4 - 8 weeks in advance.
| Microarray Workshop I - Using Microarrays to Find Differentially Expressed Genes - John Tobias |
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| Sequence Analysis Strategies I (sequence alignment) - Brian Brunk |
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A practical workshop that will address the basic questions one can ask starting with a sequence, the types of algorithms that are available, resources for running those algorithms and interpreting the results.
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| Microarray Workshop II - Beyond the Gene List - Annotation, Clustering, Sample Class Discovery, Pathway Analysis - John Tobias |
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| Functional Genomics Resources in Model Organisms - Multiple Speakers |
Each speaker will give a 20 minute presentation on functional genomics resources in their favorite organism with 10 minutes between sessions. Please feel free to attend individual presentations. The presentations will have a similar format and will address the following types of questions:
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| Vector NTI Lecture and hands-on workshop - Rob Mervis (InVitrogen) |
| Rob Mervis from InVitrogen will be here Friday, December 3 to present training sessions for VectorNTI advance, a powerful suite of sequence analysis tools. VectorNTI is available to the UPenn community via subscription to the sequence tools that PBiC provides. There will be a lecture (with question and answer times) in the morning from 9:00 - 11:30 in the BRBII/III Auditorium (registration not required) and a hands on workshop at 1:00 PM in 1311 Blockley (you must register below). We have 10 computers available (first come first served). The training room is wireless enabled so please bring your own laptop if possible. We will help you install VectorNTI so you can actively participate in the training session.
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| Vector Xpression and Pathblazer Training - Kevin Groch (InVitrogen) |
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| LEARN ABOUT DS GENE AND MACVECTOR - Accelrys |
Accelrys' easy-to-use sequence analysis solutions for Windows and Macintosh. Come to one of these sessions and experience the new wave of bioinformatics tools from Accelrys. DS Gene and MacVector provide everything you need for day-to-day sequence analysis and documentation in a single compact easy to use application;
Workshops will include demonstrations of the software, answering your questions and hands on use of these packages (bring your own wireless enabled laptop....a limited number of PCs will be available for the DS Gene session). You can even bring some of your own data to ask specific questions and begin your analyses.
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| Introduction to UNIX and PERL - PBiC Staff |
This workshop is for users new to the UNIX environment and/or Perl. We will tell you about using the UNIX command line (MacOSX is UNIX), why this is worth learning and what sorts of tools are available. The second half of this workshop will be an introduction to the perl programming language. Topics that will be covered include:
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| Using The InQuiry Sequence Analysis Web Tools - PBiC Staff |
This workshop focuses on sequence analysis using the BioTeam InQuiry tools which are available via a web browser at no charge to persons with a PennKey at https://inquiry.bioinformatics.upenn.edu/. This package has many sequence analysis programs that make a nice alternative to desktop analysis packages and in many cases exceed what one finds in a desktop package. We will present the different tools that are available and demonstrate how to use this powerful package. Tools available include:
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| Introduction to UNIX for beginners - PBiC Staff |
This workshop is for users new to the UNIX environment and should be taken before the Perl workshops if possible for users without UNIX experience. Topics that will be covered include:
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| Perl Programming Part I - PBiC Staff |
This first Perl workshop (lecture format) is intended to introduce persons to basic programming concepts that will allow them to write simple Perl scripts. Example scripts will be provided.
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| Perl Programming Part II - PBiC Staff |
A continuation of Perl Programming Part I. Should provide the basis for writing most perl scripts that manage data. We will work through some useful but short examples.
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| Perl Programming Part III (Using Objects) - PBiC Staff |
| This workshop will be focused on object oriented programming and using Perl objects. Particular emphasis will be given to using the BioPerl objects which provide much functionality for Bioinformatics applications.
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| Ingenuity Pathway Analysis - Deborah Riley, Ph.D. |
Join your colleagues for a seminar and scientific discussion focused on helping you understand biological mechanisms underlying your experimental data. Learn how scientists can simultaneously analyze multiple genomic and proteomic datasets to rapidly gain biological insight and understanding.
Scientists are using Ingenuity Pathways Analysis to extend the statistical analysis of their expression data allowing them to make better and faster decisions. The web-delivered application makes use of the Ingenuity Pathways Knowledge Base, the world’s largest curated database consisting of millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases.
Deborah Riley, Ph.D. will present a case study in which this technology is being used to gain insight into the biological functions and molecular mechanisms that distinguish different stages of prostate cancer.
For questions or more information contact Margaret DiFilippo, 609-971-8677 |
| Introduction to Homology Modeling of Protein Structure using DeepView and Swiss-Model - Yu Sun |
This workshop is for biologists who would like to build 3D model of a target protein based on the sequence similarity between the target and a “template” 3D structure. We will get you familiar with DeepView (Swiss-PDBviewer) and Swiss-Model in order to carry out tasks including:
Familiarity with other 3D structure analysis tools such as Cn3D, rasmol, VMD would be helpful but not required. For people who attended NCBI’s workshop for Cn3D, you already learned how to search for proper structure templates using NCBI tools. This workshop would help you extend that knowledge into homology model building based on selected templates. In addition, you will learn how to use DeepView, which is more powerful than Cn3D in 3D structure analysis. |
| Analyzing promoters in sets of co-expressed genes - Brian Brunk |
This workshop will focus on the analysis of gene promoters to identify transcription factor binding sites, particularly those that may be involved in the condition specific expression of a set of genes. We will explore a variety of bioinformatics tools both on the web and available at PBiC. Topics covered will include:
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| Spring Genomics Workshop - Don Baldwin |
Spring Genomics WorkshopWednesday, March 19, 2008 Free Box Lunch, Registration Required 9:30am: Proteomics – Chao-Xing Yuan, PhD 10:20am: Tissue Microarrays and Laser Capture – Daniel Martinez 11:10am: High-throughput sequencing – Don A. Baldwin, PhD Noon: Vendor Displays, Core Facility Posters, Lunch Online registration is closed. You may still check in at the BRB Auditorium on the morning of the workshop. |
| Fall Genomics Workshop - Don Baldwin |
Fall Genomics WorkshopFriday October 26, 2007 Free Box Lunch, Registration Required 9:30am: Research & Clinical Applications of Genomics Technologies – Don Baldwin, Ph.D. 10:00am: DNA copy number assays, tiling arrays – Eric Rappaport Ph.D. 10:30am: Experimental Design, Bioinformatics services – John Tobias Ph.D. 11:00am: High-throughput screening – Scott Diamond Ph.D. 11:40am: Vendor Displays Noon: Lunch, Core Facility posters, Vendor displays |
| Spring Genomics Workshop - Don Baldwin |
PROTEOMICS Chao-Xing Yuan, PhD Proteomics Core Facility Differential 2-D gel assays, chromatography and mass spectrometry methods, data analysis. SNP GENOTYPING Don Baldwin, PhD Molecular Diagnosis and Genotyping Facility Single nucleotide polymorphism genotyping using individual, multiplex and whole genome assays. TISSUE MICROARRAYS Alex Judkins, PhD CHOP Pathology Core Laboratories Creation and screening of multiplex tissue section microarrays. |
| Sequencher Workshop - Naomi Thomson |
| Sequencher DNA Sequence Analysis Workshop 1311 Blockley Hall University of Pennsylvania Tuesday Morning February 19th 10:00 – 12:00 CHOP (909 Abramson) Session Added: Tuesday Afternoon February 19th 2:00 - 4:00 or Wednesday Afternoon February 20th 2:00 - 4:00 For years Sequencher has been a favorite tool for assembly and contig editing. It still is, but Sequencher also does much more. This workshop will demonstrate both Sequencher’s foundation functions and its newer functions. The Foundation
The New
Gene Codes invites you to customize this workshop for your needs. If you have a data set that you can share, we can make this part of the workshop, or we can work with you one on one. Please write to Naomi Thomson directly to contribute data to the workshop or for an appointment. Register early, because space is limited, by clicking below on "Register for workhop." You will then be able to choose the session you wish to attend. |
| MacVector 10 - Kevin Kendall |
| Kevin Kendall, CEO of MacVector, Inc. is coming to UPenn to introduce release 10 of MacVector. The program is available as part of PBiC's Sequence Analysis Suite via subscription to the sequence tools. Please register for one of the 3 90 minute sessions listed below.
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