Training | Seminars News

Pharmacophore Modeling with Discovery Studio

An overview of the DiscoveryStudio 1.7 environment will be provided at the start. The course will cover in detail ligand based 3D pharmacophore generation, structure based pharmacophore design and database searching. Please note that there is no registration fee for this course.
 

When: June 11/12, 2007
PLEASE NOTE THAT THE SAME CLASS IS REPEATED TWICE TO ACCOMMODATE MORE USERS. PLEASE DO NOT REGISTER FOR TWO DAYS.

Time: 9:00 AM - 5:00 PM
Class Limit: 15 seats/class
Where: Building 430 Conference Room, Ft. Detrick, NCI-Frederick
To Register: http://www.abcc.ncifcrf.gov/training/train_add.php

PDF File: Agenda

Microarray Analysis Seminar

The National Cancer Institute has purchased site-wide licenses of Partek Genomics Suite, making it available to every researcher at the NCI.

Microarray data contains treatment and/or phenotype effects embedded in a sea of technical and biological noise. This seminar will demonstrate how to use proven statistical methods of experiment design and analysis of variance (ANOVA) to reliably identify biological effects of interest while controlling and removing noise due to biological and technical nuisance effects. Attendees will learn what ANOVA means, what it does, and how it can be used to isolate and remove unwanted technical and biological noise, clearly revealing the signals from the biological factors of interest. In addition, methods for analyzing cancer survival analysis data will be discussed, including Cox Regression, Kaplan-Meier analysis, and tumor classification. Finally, a variety of statistical visualizations will be used to interpret the results of the analyses.

Mr. Tom Downey, MSc., is President of Partek Incorporated. He provides statistical consulting to pharmaceutical, biotech, and government research institutes regarding the design and analysis of medical research data. Tom has performed experiment design and statistical analysis for several dozen microarray studies, including gene expression, copy number variation, regulation/methylation, and alternative splicing studies for his clients.

Partek Genomics Suite is a statistical and visual data analysis software package that can handle thousands of samples and millions of variables in a genomics experiment. Features include detection and display of alternative splice events, exon-level and copy number alterations, and mapping sites of protein/DNA interaction in ChIP on Chip visualization within the Genome Browser, as well as import and annotation capabilities for two-color arrays. Additionally, Partek GS is GeneChip-compatibleTM and supports Affymetrix gene expression arrays, exon arrays, chromosomal copy number analysis of high-density SNP Arrays, and ChIP on Chip studies for tiling arrays. Partek Incorporated is a leading provider of statistical analysis and interactive data visualization software for the scientific research community. Partek software enables researchers to quickly identify and quantify patterns in data, including data resulting from genomic and proteomic studies, high-throughput screening campaigns, and computer aided drug design.

ST. LOUIS, MO - January 11, 2007 – Partek Incorporated announced today that its genomic data analysis software, Partek Genomics Suite (Partek GS), has achieved GeneChip-compatible status for analysis of SNP Association Studies using the Affymetrix Inc. (Nasdaq: AFFX) GeneChip Mapping array system.

Partek GS, designed to import, analyze, and visualize high-dimensional genomic data, has features for analyzing SNP data including supporting single and multiple SNP association tests performed on allele, genotype, and dominant/recessive models, estimating p-values using Monte Carlo tests, and exploring copy number and LOH data in the same region. In addition, gene and SNP lists can be easily created and exported.

Partek GS is the first commercially available software tool to have achieved Affymetrix GeneChip-compatible status in the following areas: Gene Expression, Exon Expression, Chromosomal Copy Number analysis, Regulation analysis, and SNP analysis.

Using Experiment Design and Statistics to Reduce Noise Microarray Studies

When: February 20, 2007
Time: 2:30 PM
Where: Building 549 Auditorium, Ft. Detrick, NCI-Frederick

Protein Modeling in Discovery Studio Modeling 1.6 (Accelrys' Desktop Modeling Interface)

The ABCC maintains site licenses for Accelrys molecular modeling tools that are available to all NCI staff and contractors. Discovery Studio 1.6 allows access to many of the most commonly used molecular modeling tools directly from your desktop, workstation or laptop.This workshop provides an overview of protein modeling techniques available in the Discovery Studio interface 1.6. Participants of this workshop will be introduced to the basics of Homology modeling using DS Modeling 1.6. Database searching, template identification, sequence alignments leading to model building are some of the topics that will be discussed in detail in the workshop. This workshop requires a prerequisite of "Introduction to Discovery Studio Modeling 1,6", and it is strongly recommended that all new DS Modeling 1.6 users take the introductory workshop. Introduction to Discovery Studio Modeling 1.6 course is offered on Oct 17 and 18 to accommodate all the users, so, register for either Oct 17 session or Oct 18 session but not for both. Please register at the ABCC website given below.

When: October 19/20, 2006 (same session repeated on Oct 19 and 20)
PLEASE REGISTER FOR ONE DAY (Oct 19 or Oct 20) ONLY.

Time: 9:00 AM - 5:00 PM
Class Limit: 15 seats/session
Where: Building 430 Conference Room, Ft. Detrick, NCI-Frederick
To Register: http://www.abcc.ncifcrf.gov/training/train_login.php
(Prior Registration Required)
Registration will open from 10/03/2006 (Tuesday)


Information: http:/www.abcc.ncifcrf.gov/

Workshop Agenda for Protein Modeling in Discovery Studio

• Overview
• Identifying the Template(s) (Lecture)
• Hands-on Exercises
• Sequence Alignment-I (Lecture)
• Hands-on Exercise
• Sequence Alignment-I (Lecture)
• Hands-on Exercises
• Automated Homology Modeling (Lecture)
• Hands-on Exercises
• Validation and Analysis (Lecture>
• Hands-on Exercises

Pharmacophore Modeling & Database Searching using Catalyst

Advanced Biomedical Computing Center (ABCC) is hosting a class on "Pharmacophore Modeling & Database Searching using Catalyst" to the NCI/NIH community at the Fort Detrick in Frederick, MD. The class is free to participants but requires pre-registration to assure access to researchers for the hands-on training session. Registration will be filled on a first-come first-served basis.
 

When: December 13/14, 2005
Time: 1:00 PM - 5:00 PM
Where: Building 430 Conference Room, Ft. Detrick, NCI-Frederick
Instructor: K. Raghavan, Ph.D., Accelrys Inc

The class will cover the different modules of the Catalyst software suite.

Ingenuity Pathways Analysis: On-Site Training (July 19, 2005)

Funded access to Ingenuity Pathways Analysis is now available to all NCI affiliated researchers. Please use the registration link below to initiate your user account (NCI affiliated e-mail address required).

Ingenuity Pathways Analysis allows researchers to concurrently analyze multiple datasets from genomics and proteomics experimentation platforms in order to identify the key functions and pathways that distinguish one biological condition from another. This innovative technology is used to gain insights into the biological functions and molecular mechanisms that distinguish different stages of disease.

When: July 19, 2005
Time: 9:00 AM - 12:30 PM
Where: Building 430 Conference Room, Ft. Detrick, NCI-Frederick
PDF File: NCI Ingenuity License Resource
New Account Form: http://www.ingenuity.com/products/act-nci.html

Questions? Call 866.464.3684 -or- support@ingenuity.com

GeneGo Pathways/Systems Biology Presentation, Nov. 17, 2004

GeneGo's integrated data-mining suite, MetaCore 2.0, is based on a comprehensive interactive database with more than 400 functional maps of human biology. It also includes seven network-building algorithms and additional visualization tools. MetaCore's manually curated content covers many levels of functionality, from GPCRs and other receptors to signal transduction cascades, transcriptional factors, and core effector networks. The company says one of the main applications of MetaCore lies in visualization and analysis of complex experimental data, including microarray gene expression, SAGE and SNP DNA sequences, and proteomic and metabolite profiles.

When: November 17, 2004
Time: 9:00 AM - 12:00 PM
Where: Building 430 Conference Room, Ft. Detrick, NCI-Frederick
Information: http://www.genego.com/

Unique capabilities of MetaCore

• MetaCore has the largest manually curated , proprietary human database.
• MetaCore can be installed behind your firewall.
• MetaCore has the ability to display rat , mouse, yeast, worm orthologs.
• Users can import mouse chip data in to MetaCore and display it in maps.
and networks.
• Users can import Tox chip data in to MetaCore and display it in maps and networks.
• Users can import Affy and Agilent chips directly or through Genespring or Rosetta Resolver.
• MetaCore is the only platform that can concurrently visualize multiple types of data: micro array, SAGE, proteomic, Metabolomic and SNP data. (This is important as users can use other types of data to cross validate their micro array results or fill in gaps of genes that are not on the chip they ran.)
• The largest map collection, 400 consensus maps.
• A choice of 7 algorithms for building networks, shortest path, longest path, sub groups for universal network (Researchers need options as each question you ask of the data can be answered best by one of the 7 algorithms).
• 270,000 synonyms manually resolved. GeneGo has taken the time to manually develop a Thesaurus that we ship with MetaCore. This means that when a gene, protein or compound may have received several different names over the years we have all of the synonyms so MetaCore will build only one pathway.
• MetaCore is the only product that has disease filters (this allows you to focus on diseases of interest and explore impact on other diseases. We have also been told this acts as a good reference tool when researchers have been put on a new project where they know nothing about the disease. By searching MetaCore and reading references they can get up to speed quickly).
• MetaCore is the only product with tissue filters (Users can look at pathways in specific tissue such as prostate, muscle etc).
• MetaCore allows users to visualize multiple time points, dosages, treatment and diseased versus normals in the context of maps and networks.
• Users can configure coloring of microarray data (2-5 fold red, 5-10 fold green etc).
• Data mining. You don't need to start with a gene list to use MetaCore, you can explore the data through search capabilities and maps.
• MetaCore is the only product that allows you to add, change and edit pathways as well as adding your own annotation and references, internal and external on in house installations.

Ingenuity™ Pathway Seminar, Sept. 14, 2004

A new approach to comparing biological conditions; disease subtypes, time course, and dose response.
 

When: September 14, 2004
Time: 3:00 PM - 4:30 PM
Where: Building 430 Conference Room, Ft. Detrick, NCI-Frederick