Bioinformatics courses

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, Mr. Refael Kohen

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

Location: Feinberg classroom B

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

Location: Feinberg classroom B

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

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

UCSC genome browser, 2-Jan-2018

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

CRISPR design workshop, 9-Jan-2018

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. 

Introduction to R, 7-Feb-2018

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.

Introduction to Bulk RNA-Seq analysis (including Mars-seq), 14-Feb-2018

By Dr. Dena Leshkowitz (Bioinformatics Unit)

Location: Feinberg Room B

Genomatix,6-Mar-2018

By Dr. Shifra Ben-Dor

Location: Feinberg Room B

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

Practical Image Analysis for Biology (Fall semester, 2016)

By Ms. Ofra Golani, Dr. Vyacheslav Kalchenko, Dr. Reinat Nevo, Prof. Zvi Kam

Location: FGS computer classroom (B)

Bioimaging is a central set of tools in Biological research. It is interdisciplinary science which requires understanding of biology, microscopy, fluorescence probes, image processing and image analysis.   Tremendous volumes of multi-dimensional biological data are now being generated in almost every branch of biology. How to visualize and how to interpret such images in quantitative, objective and efficient way is essential knowledge for students who use bioimaging for their research.

The course will cover useful techniques and tools used for analysis of images in Biology. Topics that will be addressed include: basic concepts of digital images, visualization of multi-dimensional data, image processing in preparation for analysis, noise and image enhancement, binary operations, object/particle analysis and intensity and morphometric measurements, tracking of particles and cells movement,  colocalization and deconvolution and automatically analyzing large datasets.

We will address the issues of image ethics and proper image acquisition for image analysis.

We will introduce the students with two image analysis software: the free ImageJ/Fiji package and the commercial Imaris software. We will focus on examples and hands-on exercises that will teach a broad functionality of these tools and the concepts needed for building suitable workflow for a given application.

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:Practical Image Analysis for Biology

By Ofra Golani, Vyacheslav Kalchenko, Reinat Nevo, Noga Kozer, Zvi Kam

Location:  Feinberg computer classroom (B)

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

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

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

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

23-Dec-2015: Graphs and plots in R

By Dr. Ron Rotkopf

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.

09:00 -10:00 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.

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

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.

This workshop is expected to be overbooked - we request that only one person per group register (the workshop will be given again).

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.

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

17-May-2015: Population structure workshop

By Dr. Naama Kopelman

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.

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

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.

25-9-16: 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).

25th, 26

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

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.

Workshop objectives:

Workshop format:

Prerequisites:

7-November-2016: 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.

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

2-Jan-2017: Linux for beginners

by Kirill Kogan

Location: Feinberg Room B

Short workshop overview:

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.

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

Location: Feinberg Room B

The workshop speakers

The workshop program

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

  1. Introduction to NGS technology
  2. Experimental design
  3. Primary analysis of NGS data, from the machine to sequence files per sample
  4. Secondary analysis for the following applications:
    • RNA-seq, gene level and alternative splicing
    • ChIP-seq
    • Variant detection
    • De novo transcriptome definition
  5. Biological integration and interpretation of the data
  6. 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.
  1. General Linux OS overview.
  2. Linux command line.
  3. WEXAC cluster.

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

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

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.

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 < /br> 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:

  1. How nanopore sequencing works
  2. What makes it different
  3. The options for DNA and RNA sequencing
  4. How easy it is to scale experiments
  5. What’s involved in starting to use the technology

Host: Dr. Dena Leshkowitz

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