Courses

Upcoming FGS Courses

Essentials of RNA-seq analysis, First semester, 2023 (starting 10-Nov-2022)
Analyzing single cell sequencing data,second semester, 2023 (starting 20-Apr-2023)
Statistical analysis of research data using R, second semester, 2023 (starting 18-Apr-2023)
Data Science with Python for Beginners, second semester, 2023 (starting 29-May-2023)

Upcoming Workshops

Upcoming Lectures

Given Courses

Statistical analysis of research data using R, Spring semester, 2022 (starting 27-Mar-2022)
Bioinformatics, Spring semester, 2022 (starting 27-Mar-2022)
Data Science with Python for Beginners, Spring semester (starting 6-June-2022)
An Introduction to deep-sequencing analysis for biologists, Fall semester, 2021 (starting 24-Oct-2021)
Data Science with Python for Beginners, Spring semester (starting 24-May-2021)
Statistical analysis of research data using R, Spring semester, 2021 (starting 23-Mar-2021)
Statistical Principles In The Analysis Of Research Data, Spring semester, 2020 (starting 25-Mar, 2020)
Data Science with Python for Beginners, Spring semester, 2020 (starting 11-May, 2020)
An Introduction to deep-sequencing analysis for biologists, First semester, 2020
Bioinformatics, Spring semester, 2019 (starting 25-Mar, 2019)
Statistical Principles In The Analysis of Research Data, Spring semester, 2019 (starting 27-Mar, 2019)
Bioinformatics Analysis of Next Generation Sequence (NGS) Data, First semester (starting on 8-Nov, 2018)
An Introduction to deep-sequencing data analysis, 17-27 June, 2018
Statistical principles in the analysis of research data, Spring semester, 2018
Statistical Principles in the Analysis of Research Data, spring 2017
An Introduction to Deep-Sequencing Data Analysis, Spring 2017
Statistical Principles in the Analysis of Research Data (spring semester, 2016, Thursday, 11:15-13:00)
An Introduction to Deep-Sequencing Data Analysis (13-17.3.2016, 09:00-14:30)
FGS Lab course:An Introduction to Deep-Sequencing Data Analysis (21-25.06.2015 09:00-14:30)
FGS Lab Course:Practical Image Analysis for Biology (2015)
Statistical Principles in the Analysis of Research Data (Spring 2015)
Practical Image Analysis for Biology (Fall semester, 2016)

E-learning

Illumina Sequencing Run Guide

Transcriptome RNA-Seq Bioinformatics

Transcriptome MARS-Seq Bioinformatics

Given Workshops

1-Aug-2022: Grasping biological insights from RNA-Seq
3-May-2022: All you need to know about RNA-Seq
7-July-2021: Introduction to BioCyc website tools
30-Jun-2021: Decision trees - machine learning classification models demonstrated on biological data
22-Jun-2021: Basic introduction to Linux and the Wexac cluster for bioinformatics
24-Mar-2021: Introduction to machine learning classification demonstrated on gene expression data
4-Jan-2021: Introduction to Single Cell Sequencing Data Analysis
26-Oct-2020: Machine Learning and Deep Learning with Sklearn and TensorFlow Python Packages
28-Jul-2020: The GeneCards Suite
6-Jul-2020: UTAP: User friendly Transcriptome Analysis Pipeline
25-Jun-2020: A brief technical training on bioinformatic pipeline for MARS-seq sandbox
8-Mar-2020: Gene Set Enrichment Analysis (GSEA) – a tool for understanding the biology beyond high
1-Mar-2020: CRIPSR Design
23-Feb-2020: Introduction to R
19-Jan-2020: Basic introduction to Linux and the Wexac cluster for bioinformatics
29-Dec-2019: Expander workshop
9-Sep-2019: Introducing UTAP: User-friendly Transcriptome Analysis Pipeline
16-Jul-2019: A Workflow of Machine Learning Project via Examples: Classification and Regression
14-Apr-2019: Machine Learning and its applications in Bioinformatics
24-Feb-2019: The Genomatix Software
3-Feb-2019: UCSC Genome Browser
20-Jan-2019: Introduction to R
6-Jan-2019: CRISPR Design
31-Dec-2018: The GeneVestigator Software
23-Dec-2018: Introduction to Linux and the Wexac cluster for NGS analysis
28-Nov-2018: BioCyc website tools
15-Oct-2018: Introducing UTAP: User-friendly Transcriptome Analysis Pipeline
18-Jul-2018: Hands-on: ATAC-seq analysis
6-Jun-2018: Introduction to Linux and the Wexac cluster for NGS analysis
23-May-2018: The GeneCards Suite – databases and tools for deciphering NGS data
2-May-2018: CRISPR design workshop
13-Mar-2018: Clustering and plotting using the Partek software
14-Feb-2018: Introducing UTAP: User-friendly Transcriptome Analysis Pipeline
7-Feb-2018: Introduction to R
9-Jan-2018: CRISPR design workshop
2-Jan-2018: UCSC genome browser
1-Nov-2017: New adventures with Nanopore sequencing
12-30-Sep-2017: Bioinformatics Workshops for PIs only
5-Sep-2017: The GENEVESTIGATOR® Software
26-July-2017: Ingenuity: Discovering biology with a flexible pathway analysis tool (For Vertebrates)
18-June-2017: CRIPSR Design Workshop
3-May-2017: Unix simplified for beginners
5-7-May-2017: R based advanced methods for deep sequencing analysis
6-Feb-2017: Graphs and Plots in R
2-Jan-2017: Linux for beginners
15-Nov-2016: Ingenuity workshop
7-Nov-2016: Introduction to R
1-31-Sep-2016: Python Programming
15-Sep-2016: ChIP-Seq: Using Deep Sequencing to Discover Protein-DNA Interactions
29-March-2016:Visualization and clustering with Partek
17-Feb-2016: CRIPSR Design Workshop
20-Jan-2016: Learn How to Detect Differentially Expressed Genes from RNA-Seq Data
30-Dec-2015: Python programming workshop
23-Dec-2015: Graphs and plots in R
16-Dec-2015: Ingenuity: Discovering biology with a flexible pathway analysis tool (For Vertebrates)
2-Dec-2015: CRIPSR Design Worksho
25-Nov-2016: Learn How to Detect Differentially Expressed Genes from RNA-Seq Data
31-May-2015: CRIPSR Design Workshop
17-May-2015: Population structure workshop
10-May-2015: ChIP-Seq: Using Deep Sequencing to Discover Protein-DNA Interactions

Given Lectures

01-Nov-2022: Introduction to Illumina NGS technology
25-Oct-2021: How to design your differential gene expression experiment

Registration via BBCU Activities

Registration is usually required for our workshops, and will open near the workshop date.

First you need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events

When done, you can login to the BBCU Activities (click on the LogIn button) and register for the workshop. (click on the Register button)

Upcoming Courses

Essentials of RNA-seq analysis

by Dr. Bareket Dassa, Dr. Dena Leshkowitz, Dr. Ester Feldmesser, Dr. Gil Stelzer, Dr. Noa Wigoda

When: Thursday, 0915-1100, Benoziyo Biochemistry, room 290c, First lecture 10/11/2022

Syllabus

Introduction to RNA-Seq
Experimental design
Library preparation, Illumina sequencing & Quality Control
RNA-Seq gene level differential expression and Mars-Seq analysis
Clustering analysis on gene expression data
Functional analysis: Gene Ontology and pathways
Critical review of an example RNA-Seq paper

Analyzing single cell sequencing data

by Dr. Bareket Dassa, Dr. Dena Leshkowitz, Dr. Ester Feldmesser, Dr. Gil Stelzer, Dr. Noa Wigoda

When: Thursday, 1115-1300, FGS, Rm B, First lecture 20/4/2023

Recent advances in molecular biology, microfluidics, and computation have transformed the growing field of single-cell RNA sequencing (scRNA-seq). In addition, new approaches now encompass diverse characterization of a single cell’s such as: chromatin accessibility, spatial positioning and immunophenotype. The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data.

This course is an introduction to basic approaches in single cell RNA-sequencing (scRNA-seq) data analysis and in combination with additional modalities. It will include a hands-on exercises of common bioinformatics analysis workflows.

Experience in R programming and in analysis of bulk RNA-Seq is required.

We will cover the following topics:

Introduction to Single cell technologies
Analysing gene expression (GEX) from single cells with Cell Ranger (using Chromium 10X)
Quality control measures, normalization, clustering and more using R package Seurat
Downstream analysis of gene expression data: annotating clusters, trajectories, cell-cell communications (ligand-receptor)
Analysing multiome data i.e. GEX & ATAC-Seq using R package Signac
Immune profiling & surface protein expression
Spatial transcriptomics

Statistical analysis of research data using R

by Dr. Ron Rotkopf

When: Tuesday, 1115-1300, FGS, Rm B, First lecture 18/4/2023

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods.

No background in programming is needed.

Topics by week:

Introduction to R
Descriptive statistics
Comparing two populations: t-test.
Comparing two populations - non-parametric tests
One-way ANOVA
Multiple comparisons and contrasts
Two-way ANOVA
Experimental design - randomized block, nested, split-plot
Experimental design - repeated measures
Data transformation, power calculations
Linear regression
Correlation + selected topics

Data Science with Python for Beginners

by Dr. Ido Azuri

When: Monday,1115-1300, Ebner Auditorium, First lecture 29/5/2023

Syllabus

Weeks 1-5 Learning basic packages and programming skills in python with emphasize on data science, including:

-NumPy
Pandas
Matplotlib
SciPy Working with variables, tables, plotting, loops, and conditional statements

Week 6

Scikit-learn
Learning basic principles in machine learning and solving simple problems

Upcoming Workshops

UPcoming Lectures

Given Lectures

How to design your differential gene expression experiment, 25-Oct-2021

By Dr. Noa Wigoda

When: 10:15 - 12:00

Where: Feinberg classroom C

This lecture will give an overview of design considerations for biologists that will maximize the value of the experimental results.

It will address issues such as number of replicates, batch effect, variation, pooling and more, using relevant biological examples.

Registration for the lecture is required and open.

If you are already registered to the BBCU activities, login here: http://bip.weizmann.ac.il/activbin/events (click on the LogIn button) and then you need to register for the workshop. (click on the Register button). If it is the first time, you will need to register for the BBCU activities here: http://bip.weizmann.ac.il/activbin/events , and then login and register for the workshop.

Introduction to Illumina NGS technology, 1-Nov-2021

By Dr. Ester Feldmesser

When: 10:15 - 12:00

Where: Feinberg room C

This lecture will give an overview of the principles of Illumina library preparation and structure as well as the sequencing method (cluster generation, bridge amplification and chemistry) used by its instruments.

Registration for the lecture is required and open.

Introduction to Single-cell RNA-sequencing (scRNA-seq), 3-Jan-2022

By Dr. Gil Stelzer

When: 10:15 - 11:00

Where: Feinberg room C

In this talk we will introduce the principles of the technology used for sequencing molecules from single cells. Its advantages and limitations. We will discuss the various applications of RNA-seq in single cells, such as gene expression, immune profiling (TCR and BCR).

Given FGS Courses

Data Science with Python for Beginners (Spring 2022)

by Dr. Ido Azuri

Link to Feinberg for details

When: Monday, 11:15-13:00, first lecture 6/6/2022

The course in designed for students without or with a little experience in programming that want to gain basics skills in programming in Python. Emphasize will put on data science.After completion of the course, students will gain basics programming skills in Python and some background in data science and machine learning.

Bioinformatics

by Dr. Shifra Ben-Dor, Dr. Bareket Dassa,Dr. Ester Feldmesser, Irit Orr

When: Sunday, 14:15-16:00, FGS, Rm B, Lecture on Monday, 09:15-11:00 in wolfson auditorium. First lecture 27/3/2022

This course will teach the data and algorithms behind the most commonly used bioinformatics tools from a biological perspective. When the course is over, participants should be able to use the data and programs and make informed choices as to the program, the parameters and databases, regardless of the particular site used. Best practices (recommended sites and programs) for various biological contexts will also be taught. In the final project students will take one gene and follow through everything we did in the course on their gene of interest.

Course syllabus

Basic topics:
   Introduction to Databases
   DNA sequencing and assembly
   Pairwise comparison
   Database similarity searching
   Multiple alignment
   Motifs, patterns and profiles
   Gene Structure
   Genome databases and browsers

Additional topics (time permitting):
   Comparative genomics
   Protein secondary structure
   Gene Ontology
   Pathway Analysis
   Gene knockdown (miRNA, siRNA, and CRISPR)

Statistical analysis of research data using R (Spring 2022)

by Dr. Ron Rotkopf

When: Thursday, 10:15-12:00, first lecture 27/3/2022)

Course Syllabus:

   Introduction to R
   Descriptive statistics
   Comparing two populations: t-test
   Comparing two populations - non-parametric tests
   One-way ANOVA    Multiple comparisons and contrasts
   Two-way ANOVA
   Experimental design - randomized block, nested, split-plot
   Experimental design - repeated measures
   Data transformation, power calculations
   Linear regression
   Correlation + selected topics

An Introduction to deep-sequencing analysis for biologists (Fall semester)

by Dr. Dena Leshkowitz, Dr. Bareket Dassa, Dr. Ester Feldmesser, Dr. Gil Stelzer, Dr. Noa Wigoda, Dr. Tsviya Olender

When: Monday, 10:15-12:00, Thursday, 09:15-11:00, FGS, Rm B
First Lecture: 25/10/2021

This course is an introduction to deep sequencing analysis. The course is based on web tools. No programming skills are required.

Syllabus:

    Experimental design
    Introduction to Illumina NGS technology
    Illumina Primary Analysis
    Sequence alignment or mapping
    Alignment visualization
    Gene Expression Analysis (RNA-seq & MARS-seq)
    Clustering
    Exploratory analysis
    Functional analysis: Gene Ontology
    Functional analysis: Pathway analysis
    Assembly and quantification of transcripts from RNA-Seq data
    Long read sequencing using Oxford Nanopore Technology (ONT)and Pacific Biosciences (PacBio)
    Variant detection
    ChIP-Seq: Using High-Throughput Sequencing to Discover Protein-DNA Interactions
    ATAC-Seq: mapping chromatin accessibility
    Introduction to Single-cell RNA-sequencing (scRNA-seq)
    scRNA analysis : From the Single Cell Count Matrix to Biological Knowledge (using Seurat)
    Metagenomics overview

For more details about this course, click here

Data Science with Python for Beginners (Spring 2021)

by Dr. Ido Azuri

Link to Feinberg for details

When: Wednesday, 13:15-15:00, first lecture 25/3/2020

Statistical analysis of research data using R (Spring 2021)

by Dr. Ron Rotkopf

When: Tuesday, 11:15-13:00, first lecture 23/3/2021)

Upon successful completion of this course students should be able to:
Determine the appropriate statistical analysis for a given experimental setting.
Plan experiments while considering statistical power, sufficient sample size, and avoiding potential statistical "pitfalls". Execute a variety of common statistical tests (e.g., t-tests, ANOVA and its different variations, multiple linear regression, non-parametric analysis) using R (although the knowledge obtained will be applicable for commercial statistical software as well).
Critically review statistical analyses conducted in published papers.

Statistical Principles in the Analysis of Research Data (Spring 2020)

by Dr. Ron Rotkopf

Link to Feinberg for details

When: Wednesday, 13:15-15:00, first lecture 25/3/2020

Location: Feinberg classroom B

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R or other statistical software. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods. No background in programming is needed.

Data Science with Python for Beginners

by Dr. Ido Azuri

Link to Feinberg for details

Learning basics packages and programming skills in python with emphasize on data science and machine learning

When: Lecture Monday, 1115-1300 and Tutorials Thursday, 1115-1300 , First Lecture: 11/05/2020

An Introduction to deep-sequencing analysis for biologists

Lecturers:Dr. Dena Leshkowitz, Dr. Ester Feldmesser, Dr. Gil Stelzer, Dr. Bareket Dassa, Dr. Noa Wigoda, Dr. Tsviya Olender

Link to Feinberg for details

Course Schedule and Location

First Semester: Tuesday, 0915-1100, Wolfson Auditorium
Tutorials: Wednesday, 1115-1300, FGS, Room B
First Lecture: 05/11/2019

Course material:

This course is an introduction to deep sequencing analysis. The course is based on web tools. No programming skills are required.

Syllabus:

    Introduction to Illumina NGS technology
    NGS applications and introduction to analysis
    Illumina Primary Analysis Pipeline & Quality Control
    Illumina library preparation
    Sequence alignment to genome
    RNA-Seq gene level differential expression and Mars-seq analysis
    RNA-Seq transcript level analysis and de novo transcriptome assembly
RNA-Seq analysis for non-model organisms
    Clustering analysis on gene expression data
    Functional analysis: Gene Ontology and pathways
    Single cell RNA-Seq technology and analysis
    Epigenomic data analysis: ChIP-Seq & ATAC-Seq
    Variant detection analysis
    Long read sequencing technologies: PacBio and Nanopore
     In-house developed NGS pipelines interface
    Metagenomics overview

Bioinformatics, Spring semester, 2019 (starting 25-Mar, 2019)

Dr. Shifra Ben-Dor

When: Monday, 9:15-11:00, first lecture 25/3/2018

Location: Wolfson Auditorium

Corse Syllabus

Statistical Principles In The Analysis Of Research Data, Spring semester, 2019 (starting 27-Mar, 2019)

by Dr. Ron Rotkopf

When: Wednesday, 11:15-13:00, first lecture 27/3/2019

Location: Feinberg classroom B

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R or other statistical software. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods. No background in programming is needed.

Course Syllabus

Bioinformatics Analysis Of Next Generation Sequence (Ngs) Data, First semester, 2018

Dr. Ester Feldmesser, Dr. Dena Leshkowitz, Dr. Tsviya Olender, Dr. Hadas Keren-Shaul, Dr. Ron Rotkopf, Dr. Bareket Dassa, Dr. Noa Wigoda

When: Thursday, 9:15-12:00, first lecture 8/11/2018

Location: Feinberg classroom B

Course Syllabus

An Introduction to deep-sequencing data analysis, 17-27 June, 2018

By Dr. Ester Feldmesser, Dr. Dena Leshkowitz, Dr. Tsviya Olender, Dr. Hadas Keren-Shaul, Dr. Ron Rotkopf, Dr. Gil Stelzer

When: 17-27/6, 9:00-13:30

Location: Feinberg classroom B

Course material:

Syllabus:

    Introduction to Illumina NGS technology
    NGS applications and introduction to analysis
    Illumina Primary Analysis Pipeline & Quality Control
    Sequence alignment to genome
    RNA-Seq gene level differential expression and Mars-seq analysis
    RNA-Seq transcript level analysis and de novo transcriptome assembly
    Clustering analysis on gene expression data
    Functional analysis: Gene Ontology and pathways
    ChIP-Seq: Using NGS to Discover Protein-DNA Interactions
    Variant detection
    Additional genomic technologies: Pacbio and 10xGenomics

Statistical Principles in the Analysis of Research Data (Spring 2018)

by Dr. Ron Rotkopf

When: Monday, 11:15-13:00, first lecture 19/3/2018

Location: Feinberg classroom B

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R or other statistical software. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods. No background in programming is needed.

Topics by week:

    Introduction to R
    Descriptive statistics
    Comparing two populations: t-test
    Comparing two populations - non-parametric tests
    One-way ANOVA
    Multiple comparisons and contrasts
    Two-way ANOVA
    Experimental design - randomized block, nested, split-plot
    Experimental design - repeated measures
    Data transformation, power calculations
    Linear regression
    Correlation + selected topics

Statistical Principles in the Analysis of Research Data (Spring 2017)

By Dr. Ron Rotkopf

Location: Wolfson Auditorium

When: Thursday, 11:15-13:00, first lecture 30/03/2017

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R or commercial statistical software. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods. No background in programming is needed.

An Introduction to Deep-Sequencing Data Analysis

By Dr. Dena Leshkowitz and Dr. Ester Feldmesser

Location: FGS computer classroom (B)

When: 4-14.6.2017

This an introduction course to analysis of NGS (Next Generation Sequencing). We discuss the technology and it major applications. Our goal is to teach the basics steps of data analysis as well as how to extract biological meaning of the results.

Click here for the course materials

Statistical Principles in the Analysis of Research Data (Second Semester, 2016 on Thursday, 11:15-13:00)

By Dr. Ron Rotkopf

Location: Feinberg computer classroom (B)

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R or commercial statistical software. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods. No background in programming is needed.

An Introduction to Deep-Sequencing Data Analysis (13-17.3.2016, 09:00-14:30)

By Dr. Dena Leshkowitz and Dr. Ester Feldmesser

Location: FGS computer classroom (B)

Click here for the course materials

Statistical Principles in the Analysis of Research Data (Spring 2015)

By Dr. Ron Rotkopf

Location: Feinberg computer classroom (B)

This course aims to familiarize students with executing a variety of statistical tests: t-tests, ANOVA and its different variations, multiple linear regression and more. The principle aim of the course is to enable students to understand which analysis is applicable for each type of data, and execute the proper analyses using R or commercial statistical software. The main focus will be on usability and application of statistical knowledge in answering research questions, and less on the mathematical background of the statistical methods. No background in programming is needed.

FGS Lab course:An Introduction to Deep-Sequencing Data Analysis (21-25.06.2015 09:00-14:30)

By Dr. Ester Feldmesser, Dr. Dena Leshkowitz, Dr. Gili Friedlander, Ophir Adiv, Dr. Barak Markus

Location: Feinberg's Life Sciences Laboratory
Course Syllabus:

Given Workshops

Grasping biological insights from RNA-Seq, July 25th 2022

By: Dr.Ester Feldmesser, Dr. Noa Wigoda & Dr. Bareket Dassa, LSCF Bioinformatics unit

when: July 25th 2022, 9:00-12:00

Location: Candiotty auditorium

Description:

This workshop will cover basic concepts of gene expression clustering and functional analysis approaches.

The scope of this workshop will not include hands-on training.

Previous knowledge of basic RNA-Seq analysis will enhance your enjoyment of this workshop.

Registration is not required.

The workshop agenda:

9:00 -9:30 - Workshop overview in the context of a biological experiment

9:40 – 10:30 - Principles of hierarchical and k-means clustering

10:45 – 11:40 - Functional analysis of gene lists using Gene Ontology and pathway information

11:45 – 12:00 - Wrapping up

All you need to know about RNA-Seq, May 3rd 2022

By Dr. Dena Leshkowitz & Dr. Noa Wigoda, LSCF Bioinformatics unit

Dr. Hadas Keren-Shaul, Genomics unit

When: 9:00

where: Candiotty auditorium

Description & schedule:
RNA-Seq (including bulk Mars-seq) technology is routinely used to characterize the transcriptome and detect gene expression differences among cell types, genotypes and conditions.

The workshop on May 3rd will discuss:
9:00 -9:45 The theoretical basis for the analysis steps
9:50 – 10:35 Practical advice on protocol types & RNA quality
10:40 – 11:25 Experimental design issues demonstrated with examples from UTAP report.
UTAP: User-friendly Transcriptome Analysis Pipeline

Introduction to BioCyc website tools, July-2021

By Dr. Bareket Dassa

When: July, 2021

Where: TBA

BioCyc is an interactive web collection of organism-specific pathway/genome databases (http://www.biocyc.org/). It offers advanced tools to explore and visualize metabolic networks, for model eukaryotes and for thousands of bacterial species.
In this workshop we will demonstrate basic and advanced features of BioCyc. Starting with how to navigate the BioCyc database collection, and to visualize your omics data (transcriptomics, proteomics or metabolomics) on interactive maps of metabolic pathway. We will analyze omics data using the Omics dashboard, Pathway Collages and table tools. We will also illustrate tools for comparative analysis between species, including bacterial comparative genome browser and regulatory networks analysis. For advanced users, we will overview new features, SmartTables and the Pathway Tools Software.

Weizmann users have a free access to BioCyc collections.

Basic introduction to Linux and the Wexac cluster for bioinformatics, 22-Jun-2021

By Dr. Ester Feldmesser and Dr. Noa Wigoda

Location: Feinberg classroom B

When: 10:00 -13:00

In this workshop, we will get to know basic Linux commands and learn how to send jobs to the wexac cluster, one by one.

No previous knowledge is required.

Registration is required and open. Please use this link this link for registration and enter your name, lab and email.

Decision trees - machine learning classification models demonstrated on biological data, 30-June-2021

By Elisha Goldstein

Zoom:

When: 10:00

This workshop will have two parts:

The first part - a theoretical background will be given to image classification by deep learning algorithms.

Specifically, a pipeline for building an image classifier will be given with emphasize on convolutional neural networks (CNN) models and its components, as well as synthetic data augmentation to increase the data set size to reduce over fitting.

The second part - introducing class activation maps (CAM) which is a method to visualize the learned extracted image features that are correlated with the image classified category.

It will be demonstrated on real-word bio-medical images, and a code snippets will be given during the workshop using TensorFlow and OpenCV Python packages for deep learning and computer vision.

Introduction to machine learning classification demonstrated on gene expression data

By Elisha Goldstein

Machine learning has evolved greatly over the past two decades in both research and industry and is typically used for prediction tasks using classification models. This workshop is focused on how to construct a machine learning classifier demonstrated on an example of mRNA sequencing data downloaded from the Cancer Genomic Atlas (TCGA). The workshop will contain two parts:

10:00 – 10:30 Theoretical introduction to of basic principles in machine learning classification models: concepts, classification, data processing and construction of a machine learning model. This part will be given at beginner’s level and does not require any previous knowledge

10:30 – 11:00 Demonstration of the basic principles using Python code and Jupyter notebook as a development environment. The demonstration will be led by the lecturer, and therefore programming skills are helpful but not essential.

The notebook which will be used in the workshop is available for viewing here. In order to execute save to your Google drive (further explanations will be given in the demonstration).

For those who want to prepare for the workshop or learn by themselves about classification, attached are some links with examples and explanations:

The recordings of the lectures are found here:

https://weizmann.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=4225745b-2d9b-457c-995c-acf500a025f5>

Introduction to Single Cell Analysis (scRNA-Seq) ,Dec-2020

By Dr. Dena Leshkowitz, Dr. Gil Stelzer, Dr. Bareket Dassa and Dr. Ron Rotkopf

When: 10:00

Single-cell sequencing technologies allow the dissection of gene expression and its integration with multi-omics data at single-cell resolution, which greatly revolutionizes transcriptomic studies.

This workshop will cover the basic approaches in single cell RNA-sequencing (scRNA-seq) data analysis in combination with additional multimodal data. We will present an overview of the current 10x Genomics platform technology and applications available at the Weizmann institute. Participants will be familiarized with computational and statistical concepts in analysis of scRNA-seq using public tools.

Target audience is experimental biologists planning to design, analyze, or enhance their understanding in scRNA-seq.

The recordings of the lectures are found here:

http://dors.weizmann.ac.il/course/workshop2021/scRNA/

Machine Learning and Deep Learning with Sklearn and TensorFlow Python Packages, 26-Oct-2020

By Dr. Ido Azuri

Join from PC, Mac, Linux, iOS or Android: https://weizmann.zoom.us/j/93163450426?pwd=UVZVNDBJa0JTNUlpVzhzaFZIRmZWZz09

When: 11:00 - 12:00

In this workshop, a pipeline for solving a machine learning multi-class classification problem will be demonstrated. A synthetic unprocessed data set will be processed and modeled with basic and advanced functions of Pandas, Sklearn and TensorFlow. A short theoretical background for classification in machine learning will be introduced as well.

The workshop will start with a theoretical part that is suitable for all and will end with a hands-on part that is intended for students with background in programming (especially in Python).

28-Jul-2020: The GeneCards Suite

By Marilyn Safran, Dr. Simon Fishilevich and Dr. Ruth Barshir

Zoom: https://weizmann.zoom.us/j/92147900677?pwd=SC9nV2xzdjdwR0FoWUhPd2U3c0VCUT09

When: 10:00 - 12:00

The GeneCards® database of human genes launched in 1997, and expanded to encompass gene/disease/pathway-centric entities and relationships within the GeneCards Suite. The Suite’s comprehensive knowledgebase and tools enable navigating the universe of human biological data - genes, proteins, cells, regulatory elements, biological pathways, variants, drugs and diseases - and the connections amongst them, in research and clinical realms.

This session includes background and demos featuring GeneCards, MalaCards, PathCards, VarElect, and GeneAnalytics, as well as our latest innovations, GeneHancer and revamped gene-centered ncRNAs, and their roles in deciphering and fathoming the disease-related significance of non-coding variants identified by WGS.

6-Jul-2020: UTAP: User friendly Transcriptome Analysis Pipeline

By Dr. Dena Leshkowitz, Dr. Bareket Dassa & Dr. Noa Wigoda

Zoom: https://weizmann.zoom.us/j/97383090653

When: 9:30 - 12:30

RNA-Seq (including bulk Mars-seq) technology is routinely used to characterize the transcriptome and detect gene expression differences among cell types, genotypes and conditions. In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline (UTAP) that executes the full process on Weizmann computer cluster (WEXAC), starting from sequences and ending with a comprehensive report.

The workshop includes the theoretical basis for the analysis steps UTAP performs and a hands-on session to run the pipeline and understand the outputs it produces.

25-Jun-2020: A brief technical training on bioinformatic pipeline for MARS-seq sandbox

By Dr. Bareket Dassa

Zoom: https://weizmann.zoom.us/j/92791733489

When: 13:00-14:30

The training will cover technical explanation on the automatic processing of sequences, how to set-up UTAP (User Friendly Transcriptome Analysis Pipelines), and a brief overview on its outputs.

8-Mar-2019: Gene Set Enrichment Analysis (GSEA) – a tool for understanding the biology beyond high throughput experiments

By Dr. Ester Feldmesser

Location: Feinberg classroom B

When: 10:00 -13:00

Gene Set Enrichment Analysis (GSEA) is a computational method developed in the Broad Institute, that performs functional analysis at multiple ‘omics’ levels by integrating data from a variety of experimental platforms and providing insight into molecular and chemical interactions. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. It determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA represents an innovative method of supervised analysis that considers all of the genes in an experiment, not only those above an arbitrary cutoff in terms of fold-change or significance. It is applicable to high- throughput experiments (proteomics, siRNA screen, microarray, RNA-seq, etc.) downstream analyses in human and mammals.

Registration is required and open.

If you are already registered to the BBCU activities, login here: http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)
If it is the first time, you will need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
, and then login and register for the workshop.

1-Mar-2020: CRIPSR Design

By Dr. Shifra Ben-Dor

Location: Feinberg classroom B

When: 9:00 -13:00

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

The workshop will be a lecture and live demonstration.

Registration is required and will open near the workshop date.

If you are already registered to the BBCU activities, login here: http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)
If it is the first time, you will need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
, and then login and register for the workshop.

23-Feb-2019: Introduction to R

By Dr. Ron Rotkopf

Location: Feinberg room B

When: 10:00 - 13:00

R is a free, open-source programming language used widely for statistics and data science. This lecture will introduce the basics of R and RStudio, focusing mostly on types of data in R, reading data and manipulating data tables (a.k.a. data frames) and creating plots.

Registration is required and will open near the workshop date.

If you are already registered to the BBCU activities, login here: http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)
If it is the first time, you will need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
, and then login and register for the workshop.

19-Jan-2020: Basic introduction to Linux and the Wexac cluster for bioinformatics

By Dr. Ester Feldmesser and Dr. Noa Wigoda

Location: Feinberg classroom B

When: 14:00 -17:00

In this workshop, we will get to know basic Linux commands and learn how to send jobs to the cluster, one by one.

No previous knowledge is required.

Registration is required and will open near the workshop date.

If you are already registered to the BBCU activities, login here: http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)
If it is the first time, you will need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
, and then login and register for the workshop.

29-12-2019: Expander workshop

By Dr. Tom Hait (Tel Aviv University)

Location: Feinberg classroom B

When: 9:30 -14:30

EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression and NGS data.

It seamlessly integrates in one package all analysis steps, including:

EXPANDER provides support for analysis of human, mouse, rat, chicken, fly, zebrafish, C. elegans, S. cerevisiae, S. pombe, arabidopsis, tomato, rice, listeria, A. fumigatus and E. coli.

Registration is required and will open near the workshop date.

If you are already registered to the BBCU activities, login here: http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)
If it is the first time, you will need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
, and then login and registExpander workshop

9-Sep-2019: Introducing UTAP: User-friendly Transcriptome Analysis Pipeline,

By Dr. Dena Leshkowitz , Dr. Bareket Dassa, Dr. Noa Wigoda (Bioinformatics Unit, LSCF)

Location: Feinberg Room B

When: 13:30 - 16:00

RNA-Seq (including bulk Mars-seq) technology is routinely used to characterize the transcriptome and detect gene expression differences among cell types, genotypes and conditions. In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline: UTAP that executes the full process on Weizmann computer cluster (WEXAC), starting from sequences and ending with a comprehensive report. The workshop includes a lecture regarding the analysis steps UTAP performs and a hands on session to run the pipeline and understand the outputs it produces.

Registration is required and will open near the workshop date.

First you need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)

16-Jul-2019: A Workflow of Machine Learning Project via Examples: Classification and Regression

By Dr. Ido Azuri

By Dr. Ido Azuri

Location: Benozio room 290C

when: 10:00 - 11:00

In the workshop a general introduction to machine learning will be given. Basic definitions and ideas will be covered, via examples from bioinformatics and healthcare. This workshop is intended for audience with little or no background in machine learning and is an introduction to a series of planned meetings in machine learning with hands-on in Python.

Registration is required and will open near the workshop date.

14-Apr-2019: Machine Learning and its applications in Bioinformatics

By Dr. Ido Azuri

Location: Feinberg room B

Machine Learnig methods have great importance in sciecne and industry. In this workshop, a general introduction to machine learning will be given followed by specific applications in bioinformatics.

Registration is required and will open near the workshop date.

24-Feb-2019: The Genomatix software

By Dr. Shifra Ben-Dor

Location: Feinberg room B

When: 10:00 -13:00

The Genomatix Genome Analyzer is a suite of programs dedicated to promoter analysis, both on the single gene and gene set levels.

There are programs for transcription binding site analysis, definition of new binding sites, overrepresentation of binding sites and more.

We have a local copy of the server and accounts are available for interested Weizmann scientists.

This workshop will be an overview of the suite, with demonstrations and emphasis on the most commonly used tool

Registration is required and will open near the workshop date.

3-Feb-2019: UCSC genome browser

By Dr. Shifra Ben-Dor

Location: Feinberg Graduate School Room B

When: 10:00 -12:00

In this workshop we will cover the basic use of the UCSC Genome browser: Understanding tracks, the information available, and tips and tricks for working with the browser.This workshop will be a live demonstration. Participants who are interested can stay afterwards and are encouraged to come with their own data/questions.

Registration is required and will open near the workshop date.

20-Jan-2019: Introduction to R

By Dr. Ron Rotkopf

Location: Feinberg room B

When: 10:00 - 13:00

Registration is required and will open near the workshop date.

6-Jan-2019: CRISPR Design

By Dr. Shifra Ben-Dor

Location: Feinberg classroom B

When: 9:00 -13:00

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

The workshop will be a lecture and live demonstration.

Registration is required and will open near the workshop date.

31-Dec-2018: The GeneVestigator Software

By Irit Orr

Location: Levine meeting room (room 101)

We have recently purchased an institute license for GENEVESTIGATOR software. This software is an innovative search engine to investigate gene transcriptional regulation across thousands of experimental conditions. It nicely summarizes data by condition types such as tissues, cancers, diseases, genetic modifications, external stimuli, development for a large number of organisms (including plants and E.coli). GENEVESTIGATOR integrates manually curated and quality controlled gene expression data from public repositories, but can also integrate proprietary data. It is based on the concept of meta-profile. More advanced analyses are also possible. For example, one can search for genes specifically expressed under certain conditions, such as certain tissues, or in certain cancer types, etc. It can also search for genes sharing similar expression regulation with a target gene, or grouping genes with similar expression by means of clustering and biclustering, etc.

Registration is required and will open near the workshop date.

23-Dec-2018: Introduction to Linux and the Wexac cluster for NGS analysis

By Dr. Ester Feldmesser

Location: Feinberg Room B

In this workshop, we will get to know basic commands on Linux and learn how to send jobs to the cluster.

Registration is required and will open near the workshop date.

28-Nov-2018: BioCyc website tools

By Dr. Bareket Dassa

Location: Benozyo building, floor 2, meeting room 290

BioCyc is a collection of organism-specific pathway/genome databases (http://www.biocyc.org/). It offers advanced tools to visualize metabolic diagrams of model organisms and multiple bacterial species. In this workshop we will demonstrate how to visualize omics data (transcriptomics, proteomics or metabolomics) on interactive maps of metabolic pathway. We will navigate the pathway/genome database collection to search by gene, protein, metabolite, or pathway. We will also illustrate the bacterial comparative genome browser to compare organisms and to visualize regulatory elements. Weizmann users have a free access to BioCyc collections.

Registration is required and is now open.

15-Oct-2018: Introducing UTAP: User-friendly Transcriptome Analysis Pipeline

By Dr. Dena Leshkowitz , Dr. Barket Dassa, Dr. Noa Wigoda (Bioinformatics Unit, LSCF)

Location: Feinberg Room B

RNA-Seq(including bulk Mars-seq) technology is routinely used to characterize the transcriptome and detect gene expression differences among cell types, genotypes and conditions. In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline (UTAP) that executes the full process on Weizmann computer cluster (WEXAC), starting from sequences and ending with a comprehensive report. The workshop includes a lecture regarding the analysis steps UTAP performs and a hands on session to run the pipeline and understand the outputs it produces.

Registration is required and will open near the workshop date.

18-Jul-2018: Hands-on: ATAC-seq analysis

By Dr. Ester Feldmesser and Dr. Bareket Dassa

Location: Levine Seminar Room (101)

In this workshop we will teach how to QC and analyze ATAC-seq data, including sharing of scripts to make it easy.

This workshop is intended for people who are interested in analyzing their data by themselves.

Pre-requisites:

If you have a laptop with Secure WIFI, please bring it.

Registration is required and will open near the workshop date.

6-Jun-2018: Introduction to Linux and the Wexac cluster for NGS analysis

By Dr. Ester Feldmesser

Location: Feinberg Room B

In this workshop, we will get to know basic commands on Linux and learn how to send jobs to the cluster.

Registration is required and will open near the workshop date.

23-May-2018: The GeneCards Suite – databases and tools for deciphering NGS data

By Dr. Gil Stelzer

Location: Levine meeting room (room 101)

This workshop will introduce GeneCards and MalaCards, which unify a multitude of data sources in a gene- or disease-centric fashion. In addition, we will learn how to use GeneAnalytics for finding enriched descriptors in sets of genes and VarElect for prioritizing a list of genes in connection to phenotypes of interest.

The workshop will include both short lectures on various GeneCards suite members and hands on exercises.

Registration is required and will open near the workshop date.

2-May-2018: CRISPR design workshop

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

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

The workshop will be a lecture and live demonstration.

13-Mar-2018: Clustering and plotting using the Partek software

By Dr. Ester Feldmesser

Location: in our seminar room

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.

Registration is required.

14-Feb-2018: Introducing UTAP: User-friendly Transcriptome Analysis Pipeline

By Dr. Dena Leshkowitz (Bioinformatics Unit)

Location: Feinberg Room B

RNA-Seq technology is routinely used to characterize the transcriptome and detect gene expression differences among cell types, genotypes and conditions. In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from sequences and ending with a comprehensive report. In this workshop we will introduce UTAP developed by us and discuss how to run UTAP pipeline, the analysis steps it performs and the outputs is produces.

More information on the pipeline is available here.

Registration is required.

7-Feb-2018:Introduction to R

By Dr. Ron Rotkopf

Location: Feinberg room B

Registration is required.

9-Jan-2018: CRISPR design workshop,

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

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

The workshop will be a lecture and live demonstration.

2-Jan-2018: UCSC genome browser

By Dr. Shifra Ben-Dor

Location: Feinberg Graduate School Room B

When: January 2, 09:00 - 11:00

In this workshop we will cover the basic use of the UCSC Genome browser: Understanding tracks, the information available, and tips and tricks for working with the browser.
This workshop will be a live demonstration. Participants who are interested can stay afterwards and are encouraged to come with their own data/questions.
No Prerequisites.

Registration is required.
First you need to register for the BBCU activities here:
http://bip.weizmann.ac.il/activbin/events
(click on the LogIn button) and then you need to register for the workshop. (click on the Register button)

12-30-Sep-2017: Bioinformatics Workshops for PIs only

By the Bioinformatics unit team

Location: Levine building, Room 101

For the detailed information click here

1-Nov-2017 New adventures with Nanopore sequencing

By Jackie Evans, Knowledge Manager, Oxford Nanopore Technologies

Location: Candiotty Auditorium
When: Lecture 9:30 - 11:00

Flow cell loading demonstration 11:10- 11:30
Oxford Nanopore Technologies aims to disrupt the paradigm of biological analysis. Our technology and commercial model has already opened up DNA analysis to researchers who previously had no direct access to sequencing technologies, freeing them up to perform analyses in their own labs or in the field, and in real time. We continually improve the technology performance, make it easier to use and expand the ways in which users can access nanopore sequencing. This technology pathway is designed to enable the analysis of any living thing, by any person, in any environment.
This seminar will introduce the world's first and only nanopore DNA sequencer, the MinION which is able to sequence DNA and RNA directly, without the need for PCR. It will include examples of the MinION’s portability, the opportunities that come from real-time analysis and how long reads meet some of the challenges that exist in genomic research today. It will show how this low-cost device that has been designed to bring easy biological analyses to anyone, whether in scientific research, education or a range of real-world applications such as disease/pathogen surveillance or even microgravity biology. The MinION is in use by a thriving community of scientists in more than 70 countries, where it is enabling a myriad applications within the traditional laboratory environment and in the field.
Nanopore sequencing is full scalable through the GridION X5 and PromethION which can be used to address sequencing projects of any size. Both these systems have flow cells that can be used independently or altogether for larger projects or anything in between. Large and small projects can be run at the same time, started at different times and run for as long as necessary to generate the data required.

Join us to learn:
How nanopore sequencing works
What makes it different
The options for DNA and RNA sequencing
How easy it is to scale experiments
What’s involved in starting to use the technology

Host: Dr. Dena Leshkowitz

5-Sep-2017: The GENEVESTIGATOR® Software

By Irit Orr

Location: Levine meeting room

26-July-2017: Ingenuity: Discovering biology with a flexible pathway analysis tool (For Vertebrates)

By Dr. Ester Feldmesser

Location: Feinberg Room B

Ingenuity is a commercial tool that performs pathway and functional analysis. It 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. The tool is user-friendly and the results are shown in high quality graphics. It is applicable to high- throughput experiments (proteomics, siRNA screen, microarray, RNA-seq, etc.) downstream analyses.

Workshop Presentation

18-Jun-2017: CRIPSR Design Workshop

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

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

The program includes:

    A brief overview of CRISPR biology
    Design considerations
    On target efficiency
    Off target minimization
    Knockout vs mutation vs conditional
    Repair oligo design

3-5-17: Unix simplified for beginners

by Kirill Kogan

Location: Feinberg Room B

When: 9:00 -12:00

In this workshop, we’ll overview Linux operating system including its history, differences from Windows and why it’s beneficial for you. In addition, you’ll learn how to use Linux command line! In particular: 1) Navigating Linux file system. 2) Manipulating files and directories. 3) File system rights management and more.

    Introduction to NGS technology.
    Experimental design.
    Primary analysis of NGS data, from the machine to sequence files per sample.
    Secondary analysis for the following applications: < /br>
        RNA-seq, gene level and alternative splicing.
        ChIP-seq.
        Variant detection.
        De novo transcriptome definition.
    Biological integration and interpretation of the data.
    Additional genomic technologies.

    To be able to write programs in Python.
    To master the rich set of Python libraries and modules.
    Understand procedural control flow in Python.
    Use Object Oriented programming techniques.
    There will be 8 sessions (the last 2 are optional).
    The workshop includes approximately 40% hands on.
    Basic programming background in either a high-level language such as C, Java or a scripting language such as Shell, VBSscript, Javascript, Perl, PHP or Ruby.
    Experience with a text editor like emacs, vi, pico or notepad.
    Understanding of files and directories.

    General Linux OS overview
    Linux command line
    WEXAC cluster

5-7-March-2017: R based advanced methods for deep sequencing analysis

Location: Feinberg Room B

The workshop speakers

The workshop program

6-Feb-2017: Graphs and Plots in R

by Dr. Ron Rotkopf

Location: Feinberg Room B

When: 10:00 -13:00

In this workshop, we will demonstrate the use of the programming language "R" for creating exploratory and publication level graphs.

In the first hour, we will introduce basic data input and manipulation in R, and in the following two hours we will create plots using R base functions and the "ggplot2" package. If you already have some experience in R, and are interested only in the graphs part, you are welcome to join from the 2nd hour.

The workshop will be a lecture and a hands-on session.

2-Jan-2017: Linux for beginners

by Kirill Kogan

Location: Feinberg Room B

25-Nov-2016: Learn How to Detect Differentially Expressed Genes from RNA-Seq Data

By Dr. Dena Leshkowitz (Bioinformatics Unit)

Location: Feinberg Room B

This workshop is an introduction to the basic principles and knowhow for analyzing RNA-Seq in order to detect differentially expressed genes. We will be using Chipster, an intuitive graphical user interface, to align the reads to a genome (Tophat), quantify the genes (HTSeq) and detect differentially expressed genes (DESeq2).
9:00- 10:00 Introduction lecture
10:00-12:00 Hands-on session

Phyton programming

By Gabor Szabo

Location: Feinberg Room B

When: September 4th, 5th, 12th, 14th, 18th, 25th, 26th, 28th, 2016 at 9:30-12:30

This is a beginner on-going workshop. It is suitable for anyone wanting to use Python for developing applications, writing test for QA or using it for system administration.

15-Sep-16: ChIP-Seq: Using Deep Sequencing to Discover Protein-DNA Interactions

By Dr. Dena Leshkowitz (Bioinformatics and Biocomputing Unit)

Location: Feinberg Room B

When: September 15th, 2016 at 9:00-12:00

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).

Workshop schedule:
9:00-10:00 lecture
10:15-11:15 hands-on session
11:30-12:00 summary of the hands-on results

29-March-2016: Visualization and clustering with Partek

By Dr. Naama Kopelman

Location: Feinberg room B

17-Feb-2016: CRIPSR Design Workshop

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

In this workshop elements of CRISPR design will be presented, including demonstration of the tools and genomic considerations. The workshop will be a lecture and live demonstration.

20-Jan-2016: Learn How to Detect Differentially Expressed Genes from RNA-Seq Data

By Dr. Dena Leshkowitz (Bioinformatics Unit)

Location: Feinberg Room B

30-Dec-2015: Python programming workshop

By Dr. Naama Kopelman

Location: Feinberg room B

When: 9:00 – 12:00 (next sessions will be on Jan. 6 9:00 – 12:00, Jan. 13 9:00 – 12:00)

This workshop will introduce you to Python, a widely used and versatile programming language. Python can serve as a powerful tool for data analysis, and has a prominent place in the scientific community.

There will be 3 session for this workshop. Each session will include a lecture and a hands-on. At the end of this workshop you will be able to write simple programs yourself, mainly for text processing and data organization.
No preliminary experience is required.
** If enough students are interested, a second worshop for more advanced Python programming will be conducted.

23-Dec-2015: Graphs and plots in R

By Dr. Ron Rotkopf

When: 09:00 -10:00 lecture 10:00 - 12:00 hands-on session.

Location: Feinberg Room B

In this workshop, we will demonstrate the use of the programming language "R" for creating exploratory and publication level graphs. We will start from basic data manipulation, and use R base functions and the "ggplot2" package.

No previous experience in R is required.

15-Nov-2016: Ingenuity: Discovering biology with a flexible pathway analysis tool (For Vertebrates)

By Dr. Ester Feldmesser

Location: Levine Building , Room 101

Workshop Presentation

16-Dec-2015: Ingenuity: Discovering biology with a flexible pathway analysis tool (For Vertebrates)

By Dr. Ester Feldmesser

Location: Feinberg Room B

Workshop Presentation

2-Dec-2015: CRIPSR Design Workshop

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

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

The workshop will be a lecture and live demonstration.
Workshop Presentation

7-November-2015: Introduction to R

By Dr. Ron Rotkopf

Location: Botnar lecture hall

The lecture is planned as a preceding lecture for participants of the upcoming Bioconductor course, but it is open to anyone who is interested in beginning to work with R.

31-May-2015: CRIPSR Design Workshop

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

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

For those who participated in the CRISPR workshop on February 16, this will be an expanded version of the talk given there.
The workshop will be a live demonstration and will also have a hands-on session at the end with prepared examples for those interested, although participants are encouraged to come with their own data/questions.
This workshop is expected to be overbooked - we request that only one person per group register (the workshop will be given again). Notification of acceptance to the workshop will be sent out during the first week of March.

17-May-2015: Population structure workshop

By Dr. Naama Kopelman

Where: Feinberg Room B
When: May 17, 09:00 - 12:00

This workshop will include an introductory lecture on population structure followed by a hands-on session.

Clustering individuals into populations, based on multi-locus genotypes, has become a critical step in population genetics studies. Many different programs have been developed in order to face the challenge of dividing individuals into a predefined number of populations, K. The most widely used of these programs is STRUCTURE (Pritchard et al. 2000; Falush et al. 2003; Falush et al. 2007; Hubisz et al. 2009). Many of the STRUCTURE-like programs are stochastic, and can of produce different outcomes for replicate runs. Distinct solutions can be the result of multimodality in the solution space, or the result of label switching between clusters. In this workshop, we will discuss the use of STUCTURE, and how to make sense of multiple results for replicate runs and various K values, using some additional tools.

The hands-on session will guide the participants through prepared examples and a demonstration of some popular tools in population structure analysis Â– STRUCTURE, CLUMPP, DISTRUCT, the Evanno method, and CLUMPAK.

10-May-2015: ChIP-Seq: Using Deep Sequencing to Discover Protein-DNA Interactions

By Dr. Dena Leshkowitz

The workshop will discuss important aspects in the experiment design and how we analyse the data to find protein binding sites and determine their biological significance.
9:00-10:30 lecture
10:30-12:00 hands-on session

A simple example with fruits- Solving A Simple Classification Problem with Python — Fruits Lovers’ Edition | by Susan Li | Towards Data Science
An advanced example using a data set from the Titanic- Machine Learning with Python: Classification (complete tutorial) | by Mauro Di Pietro | Towards Data Science
- Data preprocessing and normalization
- " Identification of differential genes (including methods suitable for NGS data analysis)
- Clustering and biclustering;
- Down-stream enrichment analyses of:
  - GO functional categories
  - TF binding sites in promoter regions
  - MicroRNA sites in 3'-UTRs and
  - Biological pathways and
  - Chromosomal locations
- Network-based analysis of the expression data.
- Understanding of the library preparation protocol for ATAC-seq
- Basic knowledge of Linux
- Ready data or in process of being created
- An account on Wexac cluster

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