Bioinformatics Courses

 

Given Workshops

Upcoming Courses

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

 

Upcoming Workshops

Hands-on: ATAC-seq analysis, 18-Jul-2018, 10:00 - 12:00

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:

  • 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

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

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)

Given FGS Courses

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)

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 (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:

Here is the link to the course materials

Given Workshops

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.

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)

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.

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)

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. 

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)

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.

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)

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.

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)

7-Feb-2018:Introduction to R

By Dr. Ron Rotkopf

Location: Feinberg room B

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.

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)

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. 

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)

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

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.

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

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.

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

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 intensity values across samples and across categorical variables.

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

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

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

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

16-Dec-2015: 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

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

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).

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 – 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