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Bioinformatics Practicum 2014

Location:   GCCRI 2nd floor Classroom, Greehey Children’s Cancer Research Institute, Greehey Campus, UTHSCSA, 8403 Floyd Curl Drive, San Antonio (Web broadcast to CBI classroom, BSE 3.114, UTSA 1604 campus)

Event: A series of presentations, software demonstrations and other events on various topics of bioinformatics, such as next-generation sequencing, microarray data analysis, proteomics and metabolomics.

Registration: FREE & OPEN to UTHSCSA, UTSA and others who interested in bioinformatics topics. Please email to Eva Garcia-Rodriguez at to guarantee your seat before Noon Friday July 17, due the limit of GCCRI Classroom size.

July 21 Monday: Introduction to Bioinformatics Practicum

10:00 – 10:15 am        Logistics of Practicum  - Drs. Yidong Chen & Carolina Livi

10:15 – 11:30 am        Introduction to MATLAB and Introduction to Agilent Microarray Analysis - Dr. Yidong Chen, Professor/DEB, GCCRI
                                  [MATLAB slides (Yidong Chen)]

Lunch on your own, Refreshments will be provided

1:00 – 1:30 pm           Introduction to P20 effort - Dr. Robin Leach, Professor/CSB,  Principal Investigator of NCI P20 grant

1:30 – 3:00 pm           Intro to GeneSpring and setting up demo licenses for workshops later in the week - Dr. Carolina Livi, Agilent Technologies

3:00 – 4:00 pm           Bring your own data session

July 22 Tuesday: Introduction to Next Generation Sequencing and Data Analysis

10:00 – 10:30 am        Introduction to Genome Sequencing Facility of UTHSCSA  - Dr. Zhao Lai, Director of Genome Sequencing Facility
                                  [Genome Sequencing Facility (Zhao Lai)]

10:45 – 10:30 am        RNA-seq and Differential Gene Expression Pipeline - Dr. Yidong Chen/DEB, Dr. Yufei Huang, Professor/ECE, UTSA
                                  [NGS Data Basics Slides (Yidong Chen)]       [RNA-Seq Slides (Yufei Huang)]

Lunch on your own

2:00 – 2:45 pm           Maverix Analytic Platform Web-based RNA-seq Analysis - Dominic Trillizio, Maveric Biomics
                                 [Maverix Overview Slides (Dominic Trillizio)]

3:00 – 4:00 pm           Ingenuity Pathway Analysis

July 23 Wednesday: Next Generation Sequencing and Analysis with R 

10:00 – 11:00 am        ChIP-seq Analysis - Srikanthi R, Strand Life Sciences
                                 [ChIP Seq (Srikanthi R)

11:00 – 12:00 noon     Methyl-seq Analysis - Rohit Gupta, Strand Life Sciences
                                 [Strand NGS (Rohit Gupta)
Lunch on your own

2:00 – 3:00 pm            Introduction to R and Microarray Analysis - Dr. Daijin Ko, Professor/DMSS, UTSA
                                   [Introduction to R Slides (Thomas Girke)]   [Working with Affy Slides (Daijin Ko)]    [R Examples (Daijin Ko)]

3:00 – 4:00 pm            Bring your own data session - Dr. Yidong Chen and CBBI/GCCRI staff

July 24 Thursday: Hands on Analysis sessions

10:00 – 11:00 am        Computational methods for construction of system level understanding of biological processes - Dr. Jianhua Ruan, Associate Professor/UTSA
                                  [Gene Regulatory Networks Slides (Jianhua Ruan)]

Lunch on your own

2:00 – 3:30 pm            GeneSpring GX and PA - Shweta Shukradas, Strand Life Sciences
                                  [GeneSpring Slides (Shweta Shukradas)]

3:00 – 4:30 pm            Bring your own data session - Drs. Yidong Chen, Carolina Livi and CBBI/GCCRI staff

July 25 Friday: Proteomics and Metabolomics

10:00 – 10:15 am        Introduction to Proteomics and Metabolomics - Dr. Susan Weintraub, Professor/Biochemistry  

10:15 – 11:00 am        Metabolomics and Data Analysis/Core Facility - Dr. Xiaoli Gao, Technical Director of Metabolomics Core

11:00 – 11:45 am        Proteomics and Data Analysis/Core Facility - Dr. Susan Weintraub, Professor/Biochemistry
                                  [Introduction to Proteomics and Metabolomics Slides (Susan Weintraub and Xiaoli Gao)]

12:00 noon                  Hispanics, Cancer and Cancer Survivorship - Dr. Amelie Ramirez, Professor/DEB, IHPR
                                  [Hispanics, Cancer, and Cancer Survivorship Slides (Amelie Ramirez)]

2:00 – 3:30 pm            Combining Proteomics & Genomics Profiling Data Integrative Biology by Using Mass Profiler Professional (MPP)  - Daniel Cuthbertson, Agilent Technologies
                                   [Integrated Biology Slides (Daniel Cuthbertson)] [Template for Generic Input MPP (Daniel Cuthbertson)]

3:00 – 4:30 pm            Bring your own data session for metabolomics  - Dr. Xiaoli Gao, Proteomics/Dr. Weintraubof

Adjourn the Bioinformatics Practicum