- 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)
- 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)
- 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
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.
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 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
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.
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)
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.
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
When: Wednesday, 13:15-15:00, first lecture 25/3/2020
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.
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
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
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
Course Schedule and Location
First Semester: Tuesday, 0915-1100, Wolfson Auditorium
Tutorials: Wednesday, 1115-1300, FGS, Room B
First Lecture: 05/11/2019
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
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.
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
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
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)
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:
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.
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-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.
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)
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.
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)
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.
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)
20-Jan-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.
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)
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.
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)
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.
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-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.
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)
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.
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)
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.
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)
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.
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)
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
- 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
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- 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