The PI workshops plan:

 

Please use this link  to register to the workshops.

All workshops will be given in Levine building, room 101

 

GeneCards and its suite members VarElect, GeneAnalytics,  MalaCards and PathCards databases

 

By Dr. Gil Stelzer

When: Nov. 12th, 09:00 – 12:00

Description:

The GeneCards suite consolidates information from over 120 sources, thereupon presenting them in a gene-centric (GeneCards), disease-centric (MalaCards) and pathway-centric (Pathcards) websites.   The suite also provides analysis tools, including VarElect for gene prioritization with respect to association with diseases/phenotypes/keywords, and GeneAnalytics for impartial discovery of shared descriptors.  We will examine these tools and their output.

 

Using online databases and tools: TCGA, Xena and cBioPortal

 

By. Dr. Ron Rotkopf

When: Nov. 13th, 09:00 – 11:00

Description:

We will become familiar with several online cancer-related databases, learning how to explore specific datasets online, or download bulk data for analysis with other tools (e.g. R language).

 

Pathways analysis and demonstrations of popular tools such as:  Ingenuity, GSEA

 

By Dr. Ester Feldmesser

 

When: Nov. 13th, 13:00 – 16:00

 

Description:

Functional analysis of groups of genes sheds light on the biological meaning of gene expression changes. We will concentrate on two different tools Gene Set Enrichment Analysis (GSEA) and Ingenuity. GSEA is a computational method that determines whether an a priori defined set of genes shows significant differences between two biological states. Ingenuity is a commercial tool that helps to understand complex 'omics' data at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. It also provides insight into the causes of observed gene expression changes and into the predicted downstream biological effects of those changes.

 

 

Introduction to R language (including graphs and plots)

By Dr. Ron Rotkopf

When: Nov. 14th, 09:00 – 12:00

Description:

We will introduce basic data input and manipulation in R, and create plots using R base functions and the "ggplot2" package.

 

Clustering and plotting data (such as gene expression values) with Partek

 

By. Dr. Ester Feldmesser

When: Nov. 14th, 13:00 -16:00

Description:

In this workshop we will learn how to use the Partek® Genomics Suite®  for clustering and visualization of gene expression data. We will discuss different distance measures and clustering methods, and provide guidelines on how to select the appropriate method for your data.  In addition, we will learn to plot and visualize changes in gene expression using Volcano plots.

 

Gene regulation – promoter analysis (Genomatix)

 

By. Dr. Shifra Ben-Dor

When: Nov. 15th, 09:00 – 12:00

Description:

In this workshop we will cover the basics of computational promoter prediction, including: definition of promoters and promoter elements, description of the problem from a computational point of view, methods and tools available.

The GeneVestigator software

By Irit Orr

When: Nov. 16th, 09:00 – 11:00

Description:

Using GENEVESTIGATOR® -an innovative search engine to investigate in a single analysis gene transcriptional regulation across thousands of experimental conditions

 

Introduction to UNIX and WEXAC cluster 

 

By Kirill Kogan

When: Nov. 19th, 09:00 – 12:00

Description:

In this workshop we'll overview Linux operating system alongside practical experience of Linux command line using WEXAC servers.

 

NGS : general understanding on quality control issues and formats

 

By Dr. Gil Stelzer

When: Nov. 20th, 09:00 – 12:00

Description:

Quality control observation of NGS experiments enables the estimation of data integrity and is of great importance before subsequent analyses.  We will discuss various parameters of quality control outputs.

 

RNA-Seq gene level analysis, challenges and common algorithms and tools (including an automatic pipeline built by our unit)

 

By Dr. Dena Leshkowitz

When: Nov. 21th, 09:00 – 12:00

Description:

In this workshop we will discuss the analysis procedure from short Illumina reads to gene quantification and identification of differentially expressed genes. In the hands-on section we will run the automatic pipeline (runs STAR and DESeq2) and discuss its outputs.

 

RNA-Seq transcript level analysis, challenges and common algorithms and tools

 

By Dr. Dena Leshkowitz

When: Nov. 22nd, 09:00 – 12:00

Description:

In this workshop we will discuss the analysis procedure from short Illumina reads to transcript assembly and quantification. In the hands-on section we will use IGV browser to examine transcripts assembled by stringtie tool.

 

Mars-Seq analysis – describing the automatic pipeline that was built by our unit

 

By Refael Kohen

When: Nov. 23rd, 09:00 – 12:00

Description:

We will discuss the automatic pipeline built by us to analyze sequence data produced using Mars-seq protocol and stress the unique features in analyzing this data. The pipeline starts from demultiplexing the samples by barcodes and runs all steps required to derive differentially expressed genes.

 

ChIP-Seq analysis, challenges and common algorithms and tools

 

By Dr. Dena Leshkowitz

When: Nov. 26th, 09:00 – 12:00

Description:

This workshop will introduce the basic principles of analyzing ChIP-Seq data generated by next-generation sequencing. We will discuss the fundamentals of ChIP-seq experimental design and analysis. Following the lecture participants will complete a hands-on computer exercise using typical open-source tools (MACS, CEAS, GREAT).

 

Getting familiar with Genome Browsers (UCSC)

 

By. Dr. Shifra Ben-Dor

When: Nov. 27th, 09:00 – 12:00

Description:

In this workshop we will cover advanced uses of the UCSC Genome browser: the Table browser, custom tracks and sessions.

We will also cover basic usage of Galaxy, and the interface between Galaxy and UCSC.

 

CRISPR design

 

By. Dr. Shifra Ben-Dor

When: Nov. 28th, 09:00 – 12:00

Description:

In this workshop elements of CRISPR guide design will be presented, including demonstration of the tools and genomic considerations.

 

WIS tools for Proteomics

By. Dr. Jaime Prilusky

When: Nov. 30th , 09:00 – 11:00

Description:

We'll provide an overview of some of the tools and databases developed at Weizmann for Proteomics, how to use each tool and discuss possibilities to integrate the tools to other software or pipelines.