CLASSES & TRAINING

2017 Special Seminars and Cources:

• Biological Databases as a Research Tool Course Fall 2017. SBP Graduate Program. Dr. Andrew Hodges and Dr. Alexey Eroshkin

• Regulattice: A new SBP Portal for identifying and selecting novel cancer drivers. Dr. Alexey Eroshkin and Dr. Andrew Hodges. Come and hear about new high priority cancer targets available to SBP investigators found via an analysis of TCGA cancer samples by the Bioinformatics Shared Resource. With the advent of large-scale data repositories for cancer such as the TCGA and TCPA, newer computational approaches for identifying targetable cancer driver molecules have become increasingly available and in-demand.  We will discuss the application of our Regulattice portal to multi cancer datasets in cancer targeting.    As an example, genes guiding cancer remission versus progression in 23 major cancer types were identified using machine learning approaches applied to TCGA RNA-Seq samples.  Regulattice (http://regulattice.burnham.org) provides open access to the SBP community to share and analyze these important molecular drivers. Learn also how you can use the Regulattice portal for your own cancer target discovery projects.   Friday, September 29, 2017, 12:00pm (PST); 3:00pm (EST) Fishman Auditorium, La Jolla

2016 How-to Courses:

• Obtaining TCGA and related cancer data from selected databases: a practical guide. Tutors: Alexey Eroshkin, PhD and Andrew Hodges, PhD. Location: Building 10 Room 1308. Day: Tuesday, December 6. Time: 10:00-11:30 am (PST). Here are the pictures from the class: 1, 2 and 3. 

• Computational discovery of new disease drivers from genomics, proteomics, and metabolomics data. During this class you will learn about our customized services (and Do It Yourself options) for finding new master regulators of cancer and other diseases (VIPER, Virtual Inference of Protein-activity by Enriched Regulon analysis). Instructor: Andrew Hodges, PhD. Tuesday, May 3, 10am to 11:30am; bld. 10 rm. 1308. The link to the presentation is here. The links to the pictures are here, here and here.

2015 How-to Courses:

• Bioinformatics Class: IPA Advanced Training. Gain a better understanding of  Regulator Effects, Comparison Analysis, or Causal Network analysis capabilities with your data set. Bring your laptop. Instructor: Darryl Gietzen, Ph.D., Ingenuity Products, QIAGEN. November 17rd, 2pm to 3:30pm; bld. 10 rm. 1308. 

• Systems Biology for Starters: Reconstruction of Gene Regulatory Networks Using MetaCore. This class will introduce MetaCore, systems biology database and software suite at the beginning level. You will learn how to generate and analyze gene regulatory networks in order to produce testable hypotheses for understanding disease pathways and identifying drug targets.  MetaCore is available to ALL Sanford|Burnham researchers, with support provided by the Bioinformatics Core.  Tutor: Dr. Alexey Eroshkin. Building 10, Room 1308, Day: Tuesday, May 12, Time: 10:00-11:30 am (PST).  The link to the presentation is here. Picture of the class is here.
  

2014-2013 How-to Courses:

• BIOBASE TRANSFAC Training. Alexander Kaplun, PhD, Field Application Scientist from BIOBASE, will be providing training on how to search for individual transcription factors and miRNAs, their experimentally-characterized binding sites and regulated genes, and ChIP experiments and more  - see details below. Location: Building 10, Room 1308. Day: Tuesday, October, 21 Time: 10:00-11:30 am (PST)

• Maximizing the Biological Interpretation of Gene, Transcript & Protein Expression Data with IPA. Tutor: Dr. Darryl Gietzen, Sr. Field Application Scientist from QIAGEN. Building 10, Room 1308, Day: Tuesday, September, 16, Time: 10:00-11:30 am (PST).  You will learn about all the new IPA functionality including: Upstream Regulators Analysis, Downstream Effects Analysis, Mechanistic Networks, Comparison Analysis and Molecule Activity Predictor. The link to the presentation is here.

• Do It Yourself Systems Biology (for PIs only): The Hidden Treasure in Pathway Analysis. Tutor: Ally Perlina (new member of Bioinformatics Core). Building 10 Room 1308, July 22, 10:00-11:30 am (PST).

• Do It Yourself Systems Biology: The Hidden Treasure in Pathway Analysis. Tutor: Ally Perlina (new member of Bioinformatics Core). Building 10 Room 1308, Lake Nona: A2220 (1:00pm – 3:00pm ET). Day: Tuesday, May 20, 10:00-11:30 am (PST). Here are the pictures from the class: 1 and 2. There was great attendance at the class. Here is the link to the presentation (several slides were added).
  

• Mining cancer databases - ­ you can do it too. Tools and resources at SBMRI.  Presentation at CDSN Program Meeting. Tutor: Alexey Eroshkin, March 18, 13:00-15:00.

• TRANSFAC training. Tutor: Alexander Kaplun, PhD, Field Applications Scientist, BIOBASE Corporation. October, 8, 14:00-16:00, Bld.10, rm 1308.

• Bioinformatics class: Gene-centric bioinformatics analysis to guide cancer research. Tuesday, June 4, 10:00 am, Building 10, Room 1308. Tutors: Stacy Huang, Roy Williams and Alexey Eroshkin. During the class we will take one of human genes and walk you through several databases and bioinformatics tools to learn about changes in a gene's expression during tumorigenesis; assessing the potential impact of mutations on protein activity; distinguishing cancer-related driver mutations from passenger mutations, etc.

• Workshop: Genomics data analysis tools at your fingertips (Oncomine, GEO and CCLE). Tue, 02/12/2013, 10:00-11:00am. Stacy Huang, Roy Williams and Alexey Eroshkin. Find links to the presentations in here: Oncomine, CCLE and GEO. Once again there was great attendance at the class (see here and here).

2012 How-to Courses and Meetings:

• Statistics Primer (Dec 11, 2012, 10:00am PST) - Xiayu (Stacy) Huang. Power point presentation is here. There was great attendance at the class - see pictures 1,  2 and 3.

• Bioinformatics Users Group Meeting (Sept, 11, 2012, 10:00 am). Discussion about users experiences with our bioinformatics service. There were several valuable suggestions made at the meeting which we will try to implement soon. The picture from the meeting is here.
  

• Advanced Statistics I (April 17, 2012) - Xiayu (Stacy) Huang. Power point presentation is here. Again there was great attendance at the class.

2011 How-to Courses:

• Next-generation sequencing technology and data analysis: from reads to biology. June 8 (Wednesday) 11:00am PST, Building 10, rm 1308, Lake Nona: rm A1330, 2:00pm EST  - Jian-Liang (Jason) Li. Power point presentation is here. There was great attendance at the class - see picture1 and picture2.
  

• Microarray (and Other Omics) Data Analysis, (May 26, 10:00am PST, Bld 10 rm 1308) - Roy Williams. Lake Nona: room A2220, 1:00pm EST. Power point presentation is here. There was great attendance at the class - see picture.

• Homology, Similarity Searches and Alignments (April 5, 10:00am PST, Bld 10 rm 1308) - Kutbuddin Doctor. Lake Nona: room A2220 , 1:00pm EST. Power point presentation is here.
  

• How Statistics Can Empower Your Research (Part 2) (Feb 23, 10:00am PST, Bld 10 rm 1308) - Xiayu (Stacy) Huang. Power point presentation is here. There was great attendance at the class - see picture​.
  

• We are hosting GeneGO Seminar for MetaCore users "Unraveling Pathways to Discovery". Date and place: Sept 22, 8am-5pm. bld 10, rm 1308. For program and registration use the link http://goo.gl/JczIx. Complimentary continental breakfast and lunch provided. This is a Torrey Pines Mesa event, so registration may be limited.
  

2010 How-to Courses:

• How Statistics Can Empower Your Research (Part 1) (Dec 8, 11:00am PST, Bld 10 rm 1308) - Xiayu (Stacy) Huang. Power point presentation is here.

• NextBio integrative biological analysis (July 20, 10:00am, PST (1:00pm EST), Building 2 Room 2224)

• Phylogenetic inference (June 15, 10:00 am rm 1308, bld 10). Power point presentation is here.

• Homology, similarity search and alignments (May 5, 10:00 am rm 1308, bld 10). 
  

• Microarray data analysis. Part I. (March 9, 10:00 am rm 1308, bld 10). Power point presentation is here.
  

2009 How-to Courses:

• GeneGO Pathway analysis. Update on the newest version of MetaCore. (November, 11, 10:00 am bld 10). To get GeneGO account go to the end of BSR home page.  
  

• NextBio knowledge discovery search engine (October 6, 10:00 am, bld 10). NextBio Users guide is here.