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Upcoming Workshops


Workshops posted on this site can be attended by internal (UCR) and external (non-UCR) participants! Sign up fees are listed at the end of each event.

Introduction to R (May 13, 2011)

Date: Fri, May 13, 2011 (2:00pm - 6:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructor: Thomas Girke
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data analysis operations.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have a recent R version pre-installed. The installation instructions for the R software are provided in the installation section of the course manual. A functional wireless connection is recommended, but not essential.

Programming in R (May 14, 2011)

Date: Sat, May 14, 2011 (10:00am - 1:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructor: Thomas Girke
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of data. This workshop provides an overview of the basic knowledge for writing beginner level programs in R. The following topics will be introduced: (1) conditional executions, (2) loops, (3) writing functions, (4) techniques for improving speed/memory performance, (5) calling external software, (6) running and debugging R programs, (7) object-oriented programming in R and (8) how to build R packages. Knowledge of the R software, as introduced in the previous tutorial "Introduction to R", will be required for attending this workshop.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have a recent R version pre-installed. The installation instructions for the R software are provided in the installation section of the course manual. A functional wireless connection is recommended, but not essential.


Graphics and Data Visualization in R (May 14, 2011)

Date: Sat, May 14, 2011 (2:00pm - 5:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructor: Thomas Girke
Description: R is one of the most powerful environments for visualizing scientific data and creating beautiful publication quality graphics in a programmable and highly reproducible manner. This workshop will give an overview of the following topics: (1) introduction to R's base and grid graphics; (2) usage of high-level graphics libraries including lattice and ggplot2; (3) data pre-processing for efficient visualization; and (4) writing of functions to generate customized graphics and automating image outputs. 
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have a recent R version pre-installed. The installation instructions for the R software are provided in the installation section of the course manual. A functional wireless connection is recommended, but not essential.


Microarray Analysis with R & Bioconductor (May 15, 2011)

Date: Sun, May 15, 2011 (10:00am -1:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructor: Thomas Girke
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods, and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction to R", will be expected in this workshop.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have a recent R version pre-installed. The installation instructions for the R software are provided in the installation section of the course manual. A functional wireless connection is recommended, but not essential.


Clustering and Data Mining in R (May 15, 2011)

Date: Sun, May 15, 2011 (2:00pm - 5:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructor: Thomas Girke
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering with bootstrap, K-means, PAM, fuzzy clustering, QT, SOM, principal component analysis, multidimensional scaling, biclustering, quality assessment of clustering results, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction to R", will be required for attending this workshop.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have R, the required libraries and exercise data sets pre-installed. The installation instructions for the R software are provided on the installation page of the manual. A functional wireless connection is recommended, but not essential.


Introduction to R (May 27, 2011)

Date: Fri, May 27, 2011 (10:00am - 12:00pm)
Location: Bourns Hall A171, UC Riverside
Instructor: Thomas Girke
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data analysis operations.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have a recent R version pre-installed. The installation instructions for the R software are provided in the installation section of the course manual. A functional wireless connection is recommended, but not essential.

Linux Part I: Linux Essentials (May 27, 2011)

Date: Fri, May 27, 2011 (1:00pm - 4:00pm)
Location: Bourns Hall A171, UC Riverside
Instructors: Alex Levchuk, Tyler Backman & Thomas Girke (UCR)
Description: The majority of freely available bioinformatics software is designed for Unix/Linux-based operating systems. Basic knowledge about its usage provides free access to the most powerful and up-to-date applications in the field. The workshop will teach beginners the basic command-line syntax for running applications on large data sets on our LINUX servers and clusters from a local Windows, Mac or Linux computer. The following topics will be covered: (1) overview of the Linux operating system, (2) file system organization, (3) getting around, (4) basic Shell commands and scripts, (5) available software, (6) running software like Bowtie, BWA, BLAST, HMMER, PHYLIP, EMBOSS, etc.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course on a Linux cluster. Personal laptops are required to log remotely into the cluster. For this, all laptops need to have a functional wireless connection. In addition, they will need a terminal application and a SCP software for file exchange. Windows users should install for this purpose PuTTY and WinSCP. On Mac OS X systems, one can use the native terminal application and Fugu for file exchange. Linux systems usually have similar applications pre-configured.

Linux Part II: Using IIGB's Linux Cluster (May 27, 2011)

Date: Fri, May 27, 2011 (4:00pm - 5:00pm)
Location: Bourns Hall A171, UC Riverside
Instructors: Alex Levchuk, Tyler Backman & Thomas Girke (UCR)
Description: This seminar-style presentation will provide an introduction into the usage of the different load balancing and parallel computing tools available on IIGB's Linux cluster. A discussion will follow to determine the need for future hardware and software upgrades. PI's and users from UCR are invited to attend this event. 
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee: none
Laptop requirements: none.

Basic Analysis of Next Generation Sequencing Data with R/Bioconductor (May 28, 2011)

Date: Sat, May 28, 2011 (9:00am - 12:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructors: Tyler Backman, Rebecca Sun & Thomas Girke (UCR)
Description: R and Bioconductor provide extensive utilities for analyzing sequence data from traditional and next generation sequencing technologies (e.g. Sanger or Illumina). This workshop will cover the following topics: (1) basic sequence and string handling; (2) sequence quality assessment/filtering utilities; (3) adaptor trimming; (4) parsing sequences by location; (5) pairwise and multiple sequence alignments; (6) interacting with external short read alignments programs from R, e.g. BWA, Bowtie; (7) range operations (8) read density analysis; and (9) visualization routines. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction to R", will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course on a Linux cluster. Personal laptops are required to log remotely into the cluster. For this, all laptops need to have a functional wireless connection. In addition, they will need a terminal application and a SCP software for file exchange. Windows users should install for this purpose PuTTY and WinSCP. On Mac OS X systems, one can use the native terminal application and Fugu for file exchange. Linux systems usually have similar applications pre-configured.

Analysis of RNA-Seq, ChIP-Seq and SNP-Seq Data with R/Bioconductor (May 28, 2011)

Date: Sat, May 28, 2011 (1:00pm - 5:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructors: Tyler Backman, Rebecca Sun & Thomas Girke (UCR)
Description: This workshop will apply the knowledge covered in the basic sequence analysis event to the most common applications in the NGS field, including RNA-Seq, ChIP-Seq and SNP-Seq. This includes normalization methods and statistical tests for identifying differentially expressed genes (DEGs), peak calling methods and SNP/Indel calling methods. Basic knowledge of the R software and sequence analysis routines as introduced in the previous tutorials, will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course on a Linux cluster. Personal laptops are required to log remotely into the cluster. For this, all laptops need to have a functional wireless connection. In addition, they will need a terminal application and a SCP software for file exchange. Windows users should install for this purpose PuTTY and WinSCP. On Mac OS X systems, one can use the native terminal application and Fugu for file exchange. Linux systems usually have similar applications pre-configured.

GUI-based Exploration and Visualization of Next Generation Sequence Data (May 29, 2011)

Date: Sun, May 29, 2011 (10:00am - 1:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructors: Tyler Backman, Rebecca Sun & Thomas Girke (UCR)
Description: This workshop will introduce the basics of aligning next generation sequence (NGS) data to reference genomes/transcriptomes using cloud/web-based applications from the Galaxy service. Analysis and visualization of the read pileups along with annotation information will be performed in the free and very easy-to-use IGV genome browser from the Broad Institute. The material will be useful for both complete beginners and intermediate users (e.g. attended previous R workshop on NGS data analysis). No special computer knowledge is required for this workshop.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have a recent IGV version pre-installed. A functional wireless connection is recommended, but not essential.


Analysis of Small Molecule Data with R and Bioconductor (May 29, 2011)

Date: Sun, May 29, 2011 (2:00pm - 6:00pm)
Location: Genomics Lecture Hall, UC Riverside
Instructor: Tyler Backman & Thomas Girke
Description: This workshop introduces the ChemmineR package for mining drug-like compound and screening data sets. The new version of this R package contains functions for handling/analyzing SDF/MOL files, interfacing with PubChem, structural similarity searching, clustering of compound libraries with a wide spectrum of algorithms and utilities for managing complex compound data sets. In addition, it offers visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine Tools service and allows bidirectional communications between the two services. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. Knowledge of the R software, as introduced in the "Introduction to R" course, will be required for attending this workshop.
Manual for this workshop
Maximum number of participants: 40
How to sign up: send chosen workshop date, your name, email address, title of your position, lab affiliation (PI) and department information to thomas.girke@ucr.edu.
Registration fee*: no charge for members from registered labs and $75 for non-registered participants.
Laptop requirements: Participants will work during the course from their own laptops (Win, Mac or Linux). The laptops should have R, the required libraries and exercise data sets pre-installed. The installation instructions for the R software are provided on the installation page of the manual. A functional wireless connection is recommended, but not essential.



*Question: What are registered labs?
Answer: These are research groups that pay an annual subscription fee of $1,000 to gain access to our high performance compute infrastructure and all workshop events.





Archive of Past Workshops

Date Time Location Instructors Institution Title and Description
Nov 20, 2010
2:00-5:00pm
Genomics Lecture Hall Tyler Backman & Thomas Girke UCR
Analysis of Small Molecule Data with R and Bioconductor
Manual for this workshop
Description: This workshop introduces the ChemmineR package for mining drug-like compound and screening data sets. The new version of this R package contains functions for handling/analyzing SDF/MOL files, bioactivity data from PubChem, structural similarity searching, clustering of compound libraries with a wide spectrum of algorithms and utilities for managing complex compound data sets. In addition, it offers visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine Tools service and allows bidirectional communications between the two services. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. Knowledge of the R software, as introduced in the "Introduction to R" course, will be required for attending this workshop.
Maximum number of participants: 40
Nov 20, 2010
10:00-1:00pm Genomics Lecture Hall Thomas Girke
UCR
Introduction to R
Manual for this workshop
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data mining operations.
Maximum number of participants: 40
Oct 31, 2010
10:00-1:00pm Genomics Lecture Hall Tyler Backman, Rebecca Sun & Thomas Girke
UCR
GUI-based Exploration and Visualization of Next Generation Sequence Data
Manual for this workshop
Description: This workshop will introduce the basics of aligning next generation sequence (NGS) data to reference genomes/transcriptomes using cloud/web-based applications. Analysis and visualization of the read pileups along with annotation information will be performed in the free and very easy-to-use IGV genome browser from the Broad Institute. The material will be useful for both complete beginners and intermediate users (e.g. attended previous R workshop on NGS data analysis). No special computer knowledge is required for this workshop.
Maximum number of participants: 40
Oct 30, 2010
10:00-4:00pm Genomics Lecture Hall Tyler Backman, Rebecca Sun & Thomas Girke UCR
Analysis of Next Generation Sequencing Data with R and Bioconductor
Manual for this workshop
Description: R and Bioconductor provide extensive utilities for analyzing next generation sequence data (NGS) from technologies such as Illumina (Solexa). This workshop will cover the following topics: (1) basic sequence and string handling; (2) quality assessment utilities; (3) quality filtering; (4) adaptor trimming; (5) sequence alignments; (6) interacting with external alignments programs from R, e.g. SOAP, Maq, Bowtie; (7) read density and SNP analysis; and (8) visualization of genome-scale mapping data. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Maximum number of participants: 40
Oct 29, 2010
4:00-5:00pm Genomics Lecture Hall Alex Levchuk, Tyler Backman, Thomas Girke UCR
Linux Part II: Using IIGB's Linux Cluster
Manual for this workshop
Instructors: Alex Levchuk, Tyler Backman & Thomas Girke (UCR)
Description: This seminar-style presentation will provide an introduction into the usage of the different load balancing and parallel computing tools available on IIGB's Linux cluster. A discussion will follow to determine the need for future hardware and software upgrades. PI's and users from UCR are invited to attend this event. 
Maximum number of participants: 40
Oct 29, 2010
1:00-4:00pm Genomics Lecture Hall
Alex Levchuk, Tyler Backman, Thomas Girke UCR
Linux Part I: Linux Essentials
Manual for this workshop
Description: The majority of freely available bioinformatics software is designed for Unix/Linux-based operating systems. Basic knowledge about its usage provides free access to the most powerful and up-to-date applications in the field. The workshop will teach beginners the basic command-line syntax for running applications on large data sets on our LINUX servers and clusters from a local Windows, Mac or Linux computer. The following topics will be covered: (1) overview of the Linux operating system, (2) file system organization, (3) getting around, (4) basic Shell commands and scripts, (5) available software, (6) running software like Bowtie, Soap, BLAST, HMMER, PHYLIP, EMBOSS, etc.
Maximum number of participants: 40
Oct 3, 2010
2:00-5:00pm Genomics Lecture Hall
Thomas Girke
UCR
Clustering and Data Mining in R
Manual for this workshop
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering with bootstrap, K-means, PAM, fuzzy clustering, QT, SOM, principal component analysis, multidimensional scaling, biclustering, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 40
Oct 3, 2010
10:00-1:00pm Genomics
Lecture Hall
Thomas Girke
UCR
Microarray Analysis with R & Bioconductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 40
Oct 2, 2010
10:00-3:00pm Genomics Lecture Hall
Thomas Girke
UCR
Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of data. This workshop provides an overview of the basic knowledge for writing beginner level programs in R. The following topics will be introduced: (1) conditional executions, (2) loops, (3) writing functions, (4) techniques for improving speed/memory performance, (5) calling external software, (6) running and debugging R programs, and (7) object-oriented programming in R. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 40
Oct 1, 2010
2:00-6:00pm Genomics Lecture Hall
Thomas Girke
UCR Introduction to R
Manual for this workshop
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data mining operations.
Maximum number of participants: 40
Mar 6, 2010
2:00-5:00pm
Genomics Lecture Hall Thomas Girke UCR
Searching and Clustering Drug-like Compounds in R
Manual for this workshop
Description: This workshop introduces the ChemmineR package for mining drug-like compound and screening data sets. The R package contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of algorithms and utilities for managing complex compound data sets. In addition, it offers visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine database and allows bidirectional communications between the two services. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. Knowledge of the R software, as introduced in the "Introduction into R" course, will be required for attending this workshop.
Maximum number of participants: 40
Mar 6, 2010
10:00-12:00pm Genomics Lecture Hall Thomas Girke
UCR
Clustering and Data Mining in R
Manual for this workshop
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering with bootstrap, K-means, PAM, fuzzy clustering, QT, SOM, principal component analysis, multidimensional scaling, biclustering, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 40
Mar 5, 2010 2:00-5:00pm HMNSS1500 (Humanities) Thomas Girke
UCR
Microarray Analysis with R & Bioconductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 40
Mar 5, 2010 9:00-12:00pm Genomics Lecture Hall
Thomas Girke
UCR Introduction to R
Manual for this workshop
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data mining operations.
Maximum number of participants: 40
Feb 26, 2010 2:00-6:00pm
Genomics Lecture Hall Tyler Backman, Rebecca Sun & Thomas Girke UCR
Analysis of HT Sequencing Data with R and Bioconductor
Manual for this workshop
Description: R and Bioconductor provide extensive utilities for analyzing high-throughput sequencing data from next generation technologies, such as Illumina (Solexa). This workshop will cover the following topics: (1) basic sequence and string handling; (2) quality assessment utilities; (3) quality filtering; (4) adaptor trimming; (5) sequence alignments; (6) interacting with external alignments programs from R, e.g. SOAP, Maq, Bowtie; (7) read density and SNP analysis; and (8) visualization of genome-scale mapping data. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Maximum number of participants: 40
Feb 19, 2010
4:00-5:00pm
Genomics Lecture Hall Alex Levchuk, Tyler Backman, Thomas Girke UCR
Linux Part II: Using IIGB's Linux Cluster
Manual for this workshop
Description: This seminar-style presentation will provide an introduction into the usage of the different load balancing and parallel computing tools available on IIGB's Linux cluster. A discussion will follow to determine the need for future hardware and software upgrades. PI's and users from UCR are invited to attend this event.  
Maximum number of participants: 40
Feb 19, 2010
1:00-4:00pm Genomics Lecture Hall
Alex Levchuk, Tyler Backman, Thomas Girke
UCR
Linux Part I: Linux Essentials
Manual for this workshop
Description: The majority of freely available bioinformatics software is designed for Unix/Linux-based operating systems. Basic knowledge about its usage provides free access to the most powerful and up-to-date applications in the field. The workshop will teach beginners the basic command-line syntax for running applications on large data sets on our LINUX servers and clusters from a local Windows, Mac or Linux computer. The following topics will be covered: (1) overview of the Linux operating system, (2) file system organization, (3) getting around, (4) basic Shell commands and scripts, (5) available software, (6) running software like Bowtie, Soap, BLAST, HMMER, PHYLIP, EMBOSS, etc.
Maximum number of participants: 40
Jan 30, 2010 10:00-3:00pm
Genomics Lecture Hall Thomas Girke
UCR
Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) conditional executions, (2) loops, (3) writing functions, (4) techniques for improving speed/memory performance, (5) calling external software, (6) running and debugging R programs. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 40
Jan 29, 2010 2:00-6:00pm Genomics Lecture Hall
Thomas Girke
UCR Introduction to R
Manual for this workshop
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data mining operations.
Maximum number of participants: 40
July 23, 2009 2:30-7:00pm
1104 Batchelor Hall Tyler Backman & Thomas Girke UCR
Analysis of High-Throughput Sequencing Data with R and Bioconductor
Manual for this workshop
Description: R and Bioconductor provide extensive utilities for analyzing high-throughput sequencing data from next generation technologies, such as Illumina (Solexa). This workshop will cover the following topics: (1) basic sequence and string handling; (2) quality assessment utilities; (3) quality filtering; (4) adaptor trimming; (5) sequence alignments; (6) interacting with external alignments programs from R, e.g. SOAP, Maq, Bowtie; (7) read density and SNP analysis; and (8) visualization of genome-scale mapping data. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Maximum number of participants: 20
June 25, 2009  2:30-7:00pm 1104 Batchelor Hall
Thomas Girke
UCR
Clustering and Data Mining in R
Manual for this workshop
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering with bootstrap, K-means, PAM, fuzzy clustering, QT, SOM, principal component analysis, multidimensional scaling, biclustering, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 20
 June 5, 2009  2:30-7:00pm 1104 Batchelor Hall  Thomas Girke
UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) conditional executions, (2) loops, (3) writing functions, (4) techniques for improving speed/memory performance, (5) calling external software, (6) running and debugging R programs. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 20
April 24, 2009 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 20
March 26, 2009 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Analysis of High-Throughput Sequencing Data with R and Bioconductor
Manual for this workshop
Description: R and Bioconductor provide extensive utilities for analyzing high-throughput sequencing data from next generation technologies, such as Illumina (Solexa). This workshop will cover the following topics: (1) basic sequence and string handling; (2) quality assessment utilities; (3) quality filtering; (4) adaptor trimming; (5) sequence alignments; (6) interacting with external alignments programs from R, e.g. SOAP, Maq, Bowtie; (7) read density and SNP analysis; and (8) visualization of genome-scale mapping data. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop. Due to the computational demands of analyzing next generation sequencing data with reasonable speed, users will work during this workshop on a Linux cluster.
Maximum number of participants: 20
Feb 24, 2009 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: R (http://www.r-project.org) is a versatile data analysis environment that has a broad application spectrum in all science areas. The associated Bioconductor project provides access to hundreds of additional R packages for the analysis of modern biological and biomedical data sets, such as microarrays, next generation sequencing data, genome annotations, networks, etc. The R software is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment to prepare users with the knowledge required for the subsequent events of this R workshop series. The following topics will be covered by this R introduction: (1) command syntax, (2) basic functions, (3) data import/export, (4) data/object types, (5) graphical display, (6) usage of R packages/libraries (e.g. Bioconductor) and (7) using R for basic data mining operations.
Maximum number of participants: 20
Dec 18, 2008 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Searching and Clustering Drug-like Compounds in R
Manual for this workshop
Description: This workshop introduces the ChemmineR package for mining drug-like compound and screening data sets. The R package contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of algorithms and utilities for managing complex compound data sets. In addition, it offers visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine database and allows bidirectional communications between the two services. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. Knowledge of the R software, as introduced in the "Introduction into R" course, will be required for attending this workshop.
Maximum number of participants: 20
Nov 25, 2008 2:30-7:00pm Commons Rm 379 (Map) Thomas Girke UCR Clustering and Data Mining in R
Manual for this workshop
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering with bootstrap, K-means, PAM, fuzzy clustering, QT, SOM, principal component analysis, multidimensional scaling, biclustering, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 20
Sept 25, 2008 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) basic syntax, (2) executing R programs, (3) calling external software, (4) regular expressions, (5) writing functions, (6) control structures (loops) and (7) running R programs on Linux clusters. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 20
Aug 28, 2008 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 20
July 30, 2008 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (5) using R for data mining, (6) graphical display and (7) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 20
Feb 28, 2008 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Searching and Clustering Drug-like Compounds in R
Manual for this workshop
Description: This workshop introduces the ChemmineR package for mining drug-like compound and screening data sets. The R package contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of algorithms and utilities for managing complex compound data sets. In addition, it offers visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine database and allows bidirectional communications between the two services. The integration of chemoinformatic tools with the R programming environment has many advantages, such as easy access to a wide spectrum of statistical methods, machine learning algorithms and graphic utilities. Knowledge of the R software, as introduced in the "Introduction into R" course, will be required for attending this workshop.
Maximum number of participants: 20
Jan 31, 2008 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Clustering and Data Mining in R
Manual for this workshop
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering, bootstrap, K-means, PAM, QT, SOM, principal component analysis, multidimensional scaling, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 20
Nov 29, 2007 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of numeric data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) basic syntax, (2) executing R programs, (3) calling external software, (4) regular expressions, (5) writing functions, (6) control structures (loops) and (7) running R programs on our Linux cluster. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 20
Oct 25, 2007 2:30-7:00pm 1104 Batchelor Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 20
Sept 27, 2007 2:00-6:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (5) using R for data mining, (6) graphical display and (7) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 20
Sept 27, 2007 9:00-1:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (5) using R for data mining, (6) graphical display and (7) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 20
Apr 25, 2007 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Clustering and Data Mining in R
Manual for this workshop
Description: R contains a comprehensive set of functions and libraries for clustering large multidimensional data sets. This course will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering, bootstrap, K-means, PAM, QT, SOM, principal component analysis, multidimensional scaling, etc. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 12
Jan 25, 2007 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of numeric data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) basic syntax, (2) executing R programs, (3) calling external software, (4) regular expressions, (5) writing functions, (6) control structures (loops) and (7) running R programs on our Linux cluster. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 12
Nov 16, 2006 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description:The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 12
Oct 26, 2006 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description:The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (5) using R for data mining, (6) graphical display and (7) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 12
July 27, 2006 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of numeric data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) basic syntax, (2) executing R programs, (3) calling external software, (4) regular expressions, (5) writing functions, (6) control structures (loops) and (7) running R programs on our Linux cluster. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 12
June 8, 2006 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are freely available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 12
May 25, 2006 2:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (6) using R for data mining, (7) graphical display and (8) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 12
April 18, 2006 8:00-2:00pm Loma Linda University Bioinformatic Specialists NCBI NCBI Mini-Course
Flyer for this workshop
Description: (A) Making Sense of DNA & Protein Sequence: Participants will find a gene within a eukaryotic DNA sequence, predict the function of the implied protein product, and find a 3D modeling template for this protein sequence using NCBI resources. (B) BLAST QuickStart: A practical introduction to the BLAST family of sequence-similarity search programs. Participants will perform simple and specialized searches and learn creative uses of BLAST programs.
Organizer: Aileen Gonzales (LLU)
Maximum number of participants: 12
Mar 9, 2006 3:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of numeric data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) basic syntax, (2) executing R programs, (3) calling external software, (4) regular expressions, (5) writing functions, (6) control structures (loops) and (7) running R programs on our Linux cluster. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this workshop.
Maximum number of participants: 12
Jan 26, 2006 3:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are free and available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 12
Dec 22, 2005 3:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (6) using R for data mining, (7) graphical display and (8) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 12
Nov 22, 2005 3:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Programming in R
Manual for this workshop
Description: One of the outstanding strengths of the R language is the ease of programming extensions to automate the analysis and mining of almost any type of numeric data. This workshop provides an overview of the basic knowledge for writing beginner-level programs in R. The following topics will be introduced: (1) basic syntax, (2) executing R programs, (3) calling external software, (4) regular expressions, (5) writing functions, (6) control structures (loops) and (7) running R programs on our Linux cluster. Knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be required for attending this work shop.
Maximum number of participants: 12
Oct 27, 2005 3:00-7:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Microarray Analysis with R & BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project have become the "gold standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling data. All software components are free and available for all operating systems. This workshop will cover the following topics: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection, (4) identification of differentially expressed genes, (4) visualization of genomic information, (5) overview on clustering methods and (6) Gene Ontology (GO) analysis. Basic knowledge of the R software, as introduced in the previous tutorial "Introduction into R", will be expected in this workshop.
Maximum number of participants: 12
Sept 29, 2005 3:00-6:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction to R
Manual for this workshop
Description: The open source software R (http://www.r-project.org) has revolutionized the statistical data analysis for most bioscience and chemistry disciplines. The required time to learn the R software is well invested, since the R environment covers an unmatched spectrum of statistical tools including an efficient programming language for automating time-consuming analysis routines. The fully integrated BioConductor project contains many additional R packages, in particular for the analysis of functional genomics and microarray data. Due to their popularity, R and BioConductor are continuously updated and extended with the latest analysis tools that are available in the different research fields. The R environment is completely free and runs on all common operating systems. This workshop provides an elementary-level introduction into the R environment covering the following topics: (1) command syntax, (2) basic functions, (3) data import/export, (4) data types, (6) using R for data mining, (7) graphical display and (8) usage of R packages and libraries (e.g. BioConductor).
Maximum number of participants: 12
Jul 7, 2005 3:00-6:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction into EMBOSS: A Free Open Source Sequence Analysis Package
Manual for this workshop
Description: The only free and comprehensive sequence analysis packages is EMBOSS. It contains over 150 very useful command-line tools for analyzing DNA and protein sequences including pattern searching, phylogenetic analysis, data management, feature predictions, proteomics and more. A detailed description of all its applications can be found on this page. The workshop will provide an introduction into the functionality and usage of the different EMBOSS modules. Knowledge of the basics UNIX commands, as introduced in our 'LINUX Essentials' course, is required for attending this workshop.
Maximum number of participants: 12
Jun 23, 2005 3:00-6:30pm 1007 Noel T. Keen Hall Thomas Girke UCR LINUX Essentials
Manual for this workshop
Description: The majority of freely available bioinformatics software is designed for UNIX/LINUX-based operating systems. Basic knowledge about its usage provides free access to the most powerful and up-to-date applications in this field. The workshop will teach beginners the basic command-line syntax for running applications on large data sets on our LINUX servers and clusters from a local PC, Mac or LINUX computer. The following topics will be covered: (1) the power of UNIX/LINUX, (2) file system organization, (3) getting around, (4) the Shell, (5) available software, (6) How to run software like BLAST, HMMER, PHYLIP, EMBOSS, etc.
Maximum number of participants: 12
May 31, 2005 3:00-6:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Fast and User Friendly Chip Analysis with R and BioConductor
Manual for this workshop
Description: The statistics software R and the associated BioConductor project simplify and standardize the analysis dual color microarrays and Affymetrix chips by integrating the differnt analysis levels into one environment. The software is free and available for all operating systems. This workshop will cover the following topics: (1) a brief introduction into R, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) identification of differentially expressed genes, (4) visualization of genomic information, (5) hierarchical clustering and (6) Gene Ontology (GO) analysis.
Maximum number of participants: 12
Apr 28, 2005 1:00-4:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Expression Profiling Analysis with R and Bioconductor
Manual for this workshop
R (http://www.r-project.org) is a complete statistical software package and programming language for data manipulation, calculation and professional graphical display. The fully integrated Bioconductor project covers many additional R packages for statistical data analysis in biosciences, such as tools for the analysis of SNP and transcriptional profiling data derived from SAGE, cDNA microarrays, Affymetrix chips, etc. This workshop will be divided into two sections: the first part will provide a short introduction into R and the second part will focus on the usage of Bioconductor packages for the analysis of Affymetrix chips and dual-color microarrays (RMA, GCRMA, LIMMA, SAM, etc).
Maximum number of participants: 12
Mar 29-30, 2005 1:00-4:00pm Loma Linda University Bioinformatic Specialists NCBI NCBI Field Guide Workshop
Schedule: Download Flyer
Directions to lecture and lab rooms
Maximum number of participants: 12
Mar 17, 2005 2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Expression Profiling Analysis with R and Bioconductor
Manual for this workshop
R (http://www.r-project.org) is a complete statistical software package and programming language for data manipulation, calculation and professional graphical display. The fully integrated Bioconductor project covers many additional R packages for statistical data analysis in biosciences, such as tools for the analysis of SNP and transcriptional profiling data derived from SAGE, cDNA microarrays, Affymetrix chips, etc. This workshop will be divided into two sections: the first part will provide a short introduction into R and the second part will focus on the usage of Bioconductor packages for the analysis of Affymetrix chips and dual-color microarrays (RMA, GCRMA, LIMMA, SAM, etc).
Maximum number of participants: 12
Feb 22-23, 2005 9:00-5:00pm City of Hope Bioinformatic Specialists NCBI NCBI Workshops
First day: "A Field Guide to GenBank & NCBI Molecular Biology Resources"
Second day: "Exploring 3D Molecular Structures Using NCBI Tools & NCBI QuickScripts"
Sign up fee per computer lab session: $25
Maximum number of UCR participants: 15
Oct 29, 2004 2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction into R and Bioconductor
Manual for this workshop
R (http://www.r-project.org) is a complete statistical software package and programming language for data manipulation, calculation and professional graphical display. The fully integrated Bioconductor project covers many additional R packages for statistical data analysis in biosciences, such as tools for the analysis of SNP and transcriptional profiling data derived from SAGE, cDNA microarrays, Affymetrix chips, etc. This workshop will be divided into two sections: the first part will provide an introduction into the basic R commands under Linux and the second part will focus on the usage of Bioconductor packages for Affymetrix chip analysis (RMA, GCRMA, QC display, SAM, etc). Knowledge of the basics UNIX commands, as introduced in our 'LINUX Essentials' course, is required for attending this workshop.
Maximum number of participants: 12
July 22, 2004 2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke & Josh Lauricha UCR Large-Scale Computing on our Bioinfo LINUX Cluster
Manual for this workshop
Our facility is currently maintaining a 64-CPU LINUX cluster to significantly reduce the running time of computationally expensive bioinformatics applications. For instance HMM searches of 100,000 protein sequences against the Pfam database can be finished on this cluster within 3-4 days as opposed to 'impractical' ~200 days on a single processor machine! This seminar will provide an introduction into the usage of the different load ballancing and parallel computing systems that are available on our cluster. A discussion will follow to determine the need for future hardware growth and software requirements in this area.
Maximum number of participants: 12
July 8, 2004 2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Introduction into EMBOSS: A Free Open Source Sequence Analysis Package
Manual for this workshop
The only free and comprehensive sequence analysis packages is EMBOSS. It contains over 150 very useful command-line tools for analyzing DNA and protein sequences including pattern searching, phylogenetic analysis, data management, feature predictions, proteomics and more. A detailed description of all its applications can be found on this page. The workshop will provide an introduction into the functionality and usage of the different EMBOSS modules. Knowledge of the basics UNIX commands, as introduced in our 'LINUX Essentials' course, is required for attending this workshop.
Maximum number of participants: 12
June 24, 2004 2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR LINUX Essentials
Manual for this workshop
The majority of freely available bioinformatics software is designed for UNIX/LINUX-based operating systems. Basic knowledge about its usage provides free access to the most powerful and up-to-date applications in this field. The workshop will teach beginners the basic command-line syntax for running applications on large data sets on our LINUX servers and clusters from a local PC, Mac or LINUX computer. The following topics will be covered:
  • The power of UNIX/LINUX
  • File system organization
  • Getting around
  • The Shell
  • Available software
  • How to run software like BLAST, HMMER, PHYLIP, EMBOSS, etc.
Maximum number of participants: 12
April 15, 2004 2:00-3:30pm 1007 Noel T. Keen Hall Jennifer Le Page ChemBridge ChemBridge & CRL: Integrative Chemistry Solutions for Drug Discovery
Topics of presentation:
  • ChemBridge and CRL Corporate Overview
  • Discovery Chemistry Products
  • GPCR and Kinase Targeted Libraries
  • Discovery Chemistry Services
  • Models for Strategic Collaborations
Maximum number of participants: 12
Mar 25, 2004
Apr 5, 2004
2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR Large Scale Data Management for Biologists with the Database Software MS Access
Manual and execises for this workshop
In response to the high demand, the bioinformatics facility is offering a workshop for biologists with interest in learning a user-friendly database software for managing complex data sets from DNA array, proteomic, large-scale sequencing and other high-throughput technologies. MS Access provides a simple but efficient database environment for organizing large data sets without knowing any programming languages. It is also a very useful tool to pre-design data structures for future import into more powerful database engines like MySQL, PostgreSQL or Oracle. The software is usually preinstalled on every Windows computer with MS Office. A Mac version is not available yet. This introductory workshop will cover the following topics: data im/export, interoperability with spreadsheet programs like Excel, table relationships, filters, queries, calculations, table joining, duplicate removal, reports and forms. Active Server Pages (ASP) for designing web interfaces will not be covered.
Maximum number of participants: 12
Mar 4, 2004 2:00-4:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Chemical Genetics Seminar
Discussion of future screens and introduction into our compound database.
Jan 7, 2004 1:00-3:00pm 1007 Noel T. Keen Hall Azhar Alavi Silicon Genetics Introduction into GeneSpring
This seminar provides a general introduction into GeneSpring, a data mining package for expression profiling. New features of the latest version 6.1 will be introduced which include new filtering tools and clustering techniques.
Oct 30, 2003
Nov 20, 2003
2:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR GCG Basics (SeqWeb, SeqLab & Command Line)
Manual & Exercises for this workshop
These two workshops cover the basics on how to access GCG from SeqWeb, SeqLab and the command line. Since SeqLab is the most powerful and user-friendly GCG environment, the workshop focuses on this interface and gives an overview on the various sequence analysis tools which are available in GCG. This includes pattern searches, multiple alignments, phylogenetic trees, remote homology detection with HMMER, high-throughput sequence analysis such as BLAST searches in batch mode and how to make personal BLASTable sequence databases. Participants are encouraged to provide their own real-life problems during the exercise section. Maximum number of participants: 12
Oct 21-22, 2003 9:00-4:00pm City of Hope Bioinformaticians from NCBI NCBI NCBI Workshop
Schedule
Oct 2-3, 2003 9:00-4:00pm City of Hope Bioinformaticians from NCBI NCBI NCBI Minicourses
Schedule
Wed, July 16, 2003 2:00-5:00pm 1007 Noel T. Keen Hall Thomas Girke UCR Phred/Phrap/Consed
Manual for this workshop
April 17 & May 1, 2003 3:00-5:30pm 1007 Noel T. Keen Hall Thomas Girke UCR UNIX/LINUX Essentials for Beginners
Manual for this workshop
Topics: The Power of Unix, File System Organization, Getting Around, The Shell, Running Applications, Text Editors
March 7, 2003 Seminar: 10:30-12:00am
Workshop: 1:00-4:00pm
Seminar: Science Library, Rm 240
Workshop: Sproul Hall, Rm 2225
Richard Hughey UC Santa Cruz An Introduction to Hidden Markov Models (seminar)
Since their introduction to the biological sequence analysis community, profile hidden Markov models have become a standard for high-performance sequence search, classification, and alignment. These basic functions can also form core components of protein structure prediction and genome analysis. This tutorial presents an introduction to the process of creating and using profile hidden Markov models, followed by a discussion of the iterative search methods that enable particularly distant remote homology detection. The emphasis will be on gaining a qualitative understanding the underlying technology, with only a small amount of mathematics.

The SAM HMM Software System (hands-on workshop)
The Sequence Alignment and Modeling Software System (SAM) is the HMM system developed at UCSC in Haussler and Krogh's seminal work. It has been continuously improved since the introduction of profile HMMs, and now forms the core of our protein structure prediction efforts, and is used by many other research sites. In this workshop, we will use the SAM programs to create and examine HMMs, align sequences, and search databases. We will also use the SAM web servers for protein structure prediction. Attendees are encouraged to bring their own sequence or sequences of interest for building and using HMMs (web version).
Dec 4, 2002 9am-4pm Watkins, Rm 2101 Mike Troutman Affymerix Affymetrix Hands-On Training (limited to 12 participants)
This workshop will cover the Affymetrix image analysis tool MAS 5.0, the data mining software DMT and the database MicroDB.
Nov 8-9, 2002 9am-4pm UCR Extension Lukasz Jaroszewski & Dimitrios Morikis UCSD & UCR Protein Modeling Workshop:
1. Day: "Protein structure, domain databases, sequence and structure analysis"
2. Day: "Homology modeling and rational drug design"
Oct 8-10, 2002 8am-2pm City of Hope Bioinformaticians from NCBI NCBI NCBI Workshop (Summary):
Oct 8th: "A Field Guide to GenBank and NCBI Molecular Biology Resources"
Oct 9th: "Have a BLAST! A Practical Course on the Basic Local Alignment Search Tool (BLAST) from the NCBI"
Oct 10th: "Making Sense of DNA and Protein Sequences"
Oct 2, 2002 10am-12pm Science Library, Rm 240 Kyle O'Connor Affymerix A Demonstration of the Affymetrix Data Analysis Software
July 24, 2002 9am-3pm City of Hope Accelrys Accelrys Accelrys Biosequence Analysis Workshop
DS Gene and SeqWeb (GCG)
July 22, 2002 10am-4pm Sproul Hall, Rm 2225 InforMax InforMax Vector NTI Training
Vector NTI database structure & organization, molecule reports, maps, features, primer design, back translation, vector design & construction, import, export, BioPlot, AlignX, Contig Express.
May 29, 2002
May 22, 2002
9am - 12pm Sproul Hall, Rm 2225 Thomas Girke Center for Plant Cell Biology, UCR GCG Workshop
Manual for this workshop
Covers the basics on how to access GCG from SeqWeb, SeqLab and the command line. Since SeqLab is the most powerful and user-friendly GCG environment, the workshop will focus on this application and give an overview on the various sequence analysis tools which are available in GCG. This will include high-throughput sequence analysis such as BLAST searches in batch mode and how to make personal BLASTable sequence databases.
April 9, 2002 10am - 12pm Surge Bdg, Rm 284 Michael Gribscov San Diego Supercomputer Center Genomic analysis of plant protein kinases