bioinformatics unit department of biological services · previous achievements •fruitful...
TRANSCRIPT
Get to know us …
Bioinformatics UnitDepartment of Biological Services
Sequence analysis Biostatistical support
Image analysisNGS data analysis
Microarray analysis
Bioinformatics Team
IT & programming
Domains of Activity
Mode of work
• Consulting (first meeting free)
• Experimental design (kickoff meeting)
• Analyzing– Complete project analysis done by our team
– Guided analysis
– In your lab analysis (group meetings)
• Training, personally and in groups
• Teaching FGS courses and workshops
• Help desk
Mode of work
• Consulting
• Experimental design (kickoff meeting)
• Analyzing– Complete project analysis done by our team
– Guided analysis (for NGS)
– In your lab analysis
• Training, personally and in groups
• Teaching FGS courses and workshops
• Help desk
Guided analysis:Simplifying bioinformatics analysis
Command line operations
Graphical interface and built-in pipelines (Chipster)
Types of AnalysisAim: Find and understand the biological
meaning of the data
But.. How do we get to the aim?
We can help you -
• choose the proper tools and build proper workflows for analysis
• perform analysis using existing tools
• customize existing tools to specific data and aims
• development of new methods and algorithms
Previous achievements• Fruitful collaborations resulting in ~40 publications since
2013
• FGS courses given in 2015 (offered also in 2016):
– Statistical Principles in the Analysis of Research Data
– Practical Image Analysis for Biology
– Introduction to Deep Sequencing Analysis course
• Workshops given in 2015 (2016 to be announced):
– CRIPSR Design
– ChIP-Seq: Using Deep Sequencing to Discover Protein-DNA Interactions
– Ilastik: machine learning tool for image analysis
– Population structure
Infrastructure
• Workstations for bioinformatics applications and image analysis (@Levine bldg)
• Unix servers for intensive data analysis (local/Wexac cluster nodes)
• Software licenses for:
– Bioinformatics
– Biostatistics
– Image Analysis
• BioImg Storage Server:
– Automatically copies data from Imaging equipment & FACS at core facilities and individual labs
– Lets the users access, share, annotate the data everywhere on campus
• Managing Biological Services LIMS
BioImaging Informatics
How to store / display / enhance / quantify Image Data
Light microscopy, EM, Histology, MRI, CT
Quantitative Image Analysis
• Image data in Biology becomes larger and more important
Our aims:
• Replace subjective visual inspection and manual measurement by objective quantitative computerized image processing & analysis
• Design high throughput pipelines for image data
• Record and analyze tens of parameters per cell
• Meet reviewer requirements for quantitative measurements
Common Image Quantifications Questions
• What is the mean intensity of the green channel in wild-type and knockout ?
• What is the length or area of a structure in each cell?
• How does the intensity of the GFP change over a time course?
• How is the protein distributed, perhaps relative to a particular structure?
• How many cells, spots … are in the image?
• How fast and far does the object move ?
• How much does the green colocalize with
the red?
Biostatistical support• We provide biostatistical support at all stages of the
experiment - from planning to final analysis and presentation.• Experimental design, sample size, data organization, choosing
the proper tests, interpretation and presentation.
CyTOF analysis• CyTOF (Cytometry by Time of Flight) can characterize single
cells with dozens of probes (antibodies) per cell. • Analysis of the results requires recently developed tools for
multi-parametric data. • We provide support for these tools, either through training or
conducting the complete analysis.
Biostatistics
Possible questions:• How many samples should I use in each of my treatments?
• How do I analyze the effect of several experimental factors and/or
time points?
• Is it possible to use data from an animal that survived only half of
the experiment?
• How do I handle multiparametric data, e.g. from microarrays or
CyTOF?
Biostatistics
- Differential gene expression analysis
- Clustering of genes/conditions
- Mining and reanalysis of microarray data from published
studies (GEO)
- Comparative analysis of multiple microarray experiments at the
gene and pathway levels
Microarray Analysis
What can NGS do for you?
mRNA expression and discovery
Mutation discovery
Sequencing novel genomes
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Alternative splicing and allele specific expression
Protein-DNA interactions
Next Generation Sequencing Tools by Applications
RNA-SeqRSEM, DESeq,
CufflinksTrinity …
ChIP-SeqMACS, HOMER, Meme-
ChIP, CEAS, GREAT …
Genomic VariationIGV, VCFtools,
FreeBayes, SAMtools, GATK, Plink
MetagenomicsMetalook, Metamine, Metastats, MEGAN …
MappingBowtie, BWA, STAR, TopHat
NGS raw reads QC: fastqc, FastQ…
De novo Assembly
Velvet, Newbler …
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CLASSICAL BIOINFORMATICS
DNA
RNA
PROTEIN
Basic Tools for all:
Database SearchesAlignments
DNA Analyses
Genome Browsers Comparative Genomics
Genomic Primer Design Gene Prediction
Gene Structure
Sanger SequenceTroubleshooting
Phylogenetics
SNP Interpretation CRISPR
RNA Analyses
siRNA
Cloning/Plasmid Design
Primer Design Restriction Mapping
Splice Variants
Sanger Sequence Troubleshooting
miRNA
Long non-coding RNA
Expression3’ UTR signals
EST/gene building
Secondary Structure
Protein Analyses
Protein-protein interactions Subcellular Localization
Antigen Design
Motif Finding/Definition Secondary Structure
Post-translational modifications
Phylogenetics
Transcriptional Control(DNA-Protein-RNA interactions)
Promoter Analyses
Transcription Start Site Definition
Transcription Factor Binding Site Prediction
Conservation
Transcription Factor Binding Site Definition
SNP Interpretation
Site-licenses for software packages
• Sequence analysis:
Lasergene, MacVector, Sequencher, SnapGene
• Promoter analysis:
Genomatix Genome Analyzer (GGA)
• Pathways and system analysis:
Ingenuity – IPA Data Analysis
• Microarray and NGS statistical analysis
PARTEK Genomics Suite
• Image Analysis
Imaris, AutoQuant, Volocity, Analyze, Avizo (by CRS), Arivis
• Tool for studying publicly available expression data (GEO)
GenVestigator
Bioinformatics Unit - Contacts
• Programming projects and programming help: Dr. Jaime Prilusky
• Genomics, Promoter analysis, Sequence analysis and Phylogenetics: Dr. Shifra Ben-Dor
• High-throughput genomics and Next-generation sequencing: Dr. Ester Feldmesser, Dr. Dena Leshkowitz and Dr. Naama Kopelman
• Microarray analysis, Sequence analysis, software installation, general issues: Irit Orr
• Biostatistical support: Dr. Ron Rotkopf
• BioImaging analysis: Ofra Golani
• Infrastructure: Ofra Golani (image related), Irit Orr (bioinformatics related), Kiril Kogan, Jaime Prilusky
Head of unit:
Dr. Dena Leshkowitz (x6330)
Project coordinator:
Irit Orr (x2470)
The End
… and hopefully the beginning of collaboration on your projects!
Links to our websites:
http://www.weizmann.ac.il/Biological_Services/bioinformatics-about
http://bip.weizmann.ac.il/
http://www.weizmann.ac.il/vet/IC/informatics/about-service
General Information:
Sequence Analysis (tools):
Image Analysis:
GCK (gene construction kit) eliminates tedious examination
of DNA sequence data by automatically identifyingopen reading frames (ORF's), keeping track of sticky ends during cutting and pasting of restriction enzyme digestionfragments, assisting withPCR primer design, and enabling comprehensive annotation of DNA sequence features. This DNA analysis software allows multiple files to be opened and displayed simultaneously, allowing DNA sequences to easily be copied and pasted between plasmids and vectors to represent real-world DNA cloning protocols. The Gene Construction Kit software is available for both Windows and Macintosh users.
MacVector Major Features:Graphical Sequence Editing, Gateway and Topo CloningAuto AnnotationPrimer DesignDNA AnalysisProtein AnalysisDatabase SearchingMultiple Sequence AlignmentSequence Assembly
Site-licenses for software packages
Sequencher features:Sequence editingSequence trimmingSequence assemblyAssemble o referenceMultiple alignmentRestriction mappingConfidence valueSNP detectionAutomated analysis
SnapGene for Cloning features:Gibson Assembly®Restriction cloningPCR & MutagenesisAgarose Gel ElectrophoresisEnzyme SitesPrimersORFsChromosome–size sequencing
Ingenuity – IPA Data Analysis IPA Core Analysis has multiple ways of relating the molecules in your dataset to the bodyof information in the Ingenuity Knowledge Base. Biological functions and diseases that are over-represented in your data, and the predicted directional effects on these functions and diseases.Signaling and metabolic canonical pathways enriched in your data.Predicted upstream regulators that might explain the changes observed in your data.Molecular networks (algorithmically generated pathways describing potential molecular interactions in your experimental system)
PARTEK Genomics SuitePartek Genomics Suite is a comprehensive suite of advanced statistics andinteractive data visualization specifically designed to reliably extract biologicalsignals from noise and includes all of the functionality of the Discovery Suite.Designed for high-dimensional genomic studies containing thousands of samples,Partek GS is fast, memory efficient and will analyze large data sets on a personalcomputer. It supports a complete workflow including convenient data access tools,identification and annotation of important biomarkers, and construction andvalidation of predictive diagnostic classification systems.
AcknowledgmentsSource of Images (slides 2,5,9)
• Confocal florescence microscopy: Source: Nature of Nature
• Histology: Source: central microscopy Iowa
• Light microscopy: Phase, DIC. Source: Nikon Microscopy
• FIB-SEM: Ilana Sabanay, Elior Peles, Alon Weiner
• MRI: Michal Neeman lab