Data Management Planning workshop for new Life Science Projects
Slides from Data Management Planning online workshop for Life Science Projects for researchers
Scientific topics: Data management
Operations: Data retrieval, Data handling, Deposition
Keywords: data management plan, NeLS, TSD, metadata, sensitive, data publication, data protection, storage, identifiers, DMP, licensing, Compliance, data life cycle - collect, data life cycle - reuse, data life cycle - analyse, data life cycle - process, data life cycle - preserve, data life cycle - share, data life cycle - plan
Resource type: Slides
Data Management Planning workshop for new Life Science Projects
https://doi.org/10.5281/zenodo.4971754
http://tess.elixir-uk.org/materials/data-management-planning-workshop-for-new-life-science-projects
Slides from Data Management Planning online workshop for Life Science Projects for researchers
Erik Hjerde
Marta Eide
Korbinian Bösl
Jenny Ostrop
Ingrid Heggland
Solveig Fossum-Raunehaug
Agata Bochynska
Lars Figenschou
Nazeefa Fatima
Espen Åberg
Eivind Coward
Federico Bianchini
Data management
data management plan, NeLS, TSD, metadata, sensitive, data publication, data protection, storage, identifiers, DMP, licensing, Compliance, data life cycle - collect, data life cycle - reuse, data life cycle - analyse, data life cycle - process, data life cycle - preserve, data life cycle - share, data life cycle - plan
Professor
PhD candidate
Postdoctoral researcher
Researcher
data steward / data manager
data manager
Senior scientist/ Principal investigator
Life sciences
Statistics - Interval-Wise Testing for omics data
Statistical Analyses for omics data
Questions of the tutorial:
- How to visualize high-resolution omics data in different groups of genomic regions?
- How to evaluate differences in high-resolution omics data between groups of genomic regions?
- How to detect locations and scales at which the...
Statistics - Interval-Wise Testing for omics data
http://galaxyproject.github.io/training-material/topics/statistics/tutorials/iwtomics/tutorial.html
http://tess.elixir-uk.org/materials/statistics-interval-wise-testing-for-omics-data
Statistical Analyses for omics data
Questions of the tutorial:
- How to visualize high-resolution omics data in different groups of genomic regions?
- How to evaluate differences in high-resolution omics data between groups of genomic regions?
- How to detect locations and scales at which the significant effects unfold?
Objectives of the tutorial:
- Pre-process high-resolution omics data
- Create pointwise boxplots corresponding to different groups of genomic regions
- Perform the Interval-Wise Testing between two groups of genomic regions
- Visualize and inspect test results
- Detect relevant locations and scales
marziacremona
fabio-cumbo
Assembly - Making sense of a newly assembled genome
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - Making sense of a newly assembled genome
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.html
http://tess.elixir-uk.org/materials/assembly-making-sense-of-a-newly-assembled-genome
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I just assembled a genome. How does it compare with already sequenced genomes?
- How do I find rearranged, inserted, or deleted regions?
Objectives of the tutorial:
- Identification of the most closely related genome to my new assembly
- Perform sequence comparison to locate rearrangements
- Identify genes located in deletions
nekrut
delphine-l
Genome Annotation - Genome annotation with Prokka
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile...
Genome Annotation - Genome annotation with Prokka
http://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html
http://tess.elixir-uk.org/materials/genome-annotation-genome-annotation-with-prokka
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Questions of the tutorial:
- How to annotate a bacterial genome?
- How to visualize annoted genomic features?
Objectives of the tutorial:
- Load genome into Galaxy
- Annotate genome with Prokka
- View annotations in JBrowse
annasyme
tseemann
slugger70
Genome Annotation - Genome Annotation
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Genome Annotation - Genome Annotation
http://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/genome-annotation/tutorial.html
http://tess.elixir-uk.org/materials/genome-annotation-genome-annotation
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
joachimwolff
erxleben
bgruening
Variant Analysis - Mapping and molecular identification of phenotype-causing mutations
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- What is mapping-by-sequencing?
- How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?
Objectives of the tutorial:
- Use joint...
Variant Analysis - Mapping and molecular identification of phenotype-causing mutations
http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html
http://tess.elixir-uk.org/materials/variant-analysis-mapping-by-sequencing
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- What is mapping-by-sequencing?
- How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?
Objectives of the tutorial:
- Use joint variant calling and extraction to facilitate variant comparison across samples
- Perform variant linkage analyses for phenotypically selected recombinant progeny
- Filter, annotate and report lists of variants
wm75
Variant Analysis - Microbial Variant Calling
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How do we detect differences between a set of reads from a microorganism and a reference genome
Objectives of the tutorial:
- Find variants between a reference genome and a set of...
Variant Analysis - Microbial Variant Calling
http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html
http://tess.elixir-uk.org/materials/variant-analysis-microbial-variant-calling
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How do we detect differences between a set of reads from a microorganism and a reference genome
Objectives of the tutorial:
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
- Determine the effect of those variants on genomic features
- Understand if the SNP is potentially affecting the phenotype
annasyme
slugger70
tseemann
Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
Questions of the tutorial:
- Why is a Hi-C analysis useful?
- What is...
Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html
http://tess.elixir-uk.org/materials/epigenetics-hi-c-analysis-of-drosophila-melanogaster-cells-using-hicexplorer
DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
Questions of the tutorial:
- Why is a Hi-C analysis useful?
- What is 'chromosome conformation capture'?
- What are main steps in order to generate and plot a Hi-C contact matrix?
joachimwolff
fidelram
vivekbhr
polkhe
Variant Analysis - Calling variants in non-diploid systems
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How does frequency of mitochondrial polymorphisms change from mother to child?
Objectives of the tutorial:
- Using Galaxy's main site we will see how to call variants in bacteria,...
Variant Analysis - Calling variants in non-diploid systems
http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html
http://tess.elixir-uk.org/materials/variant-analysis-calling-variants-in-non-diploid-systems
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How does frequency of mitochondrial polymorphisms change from mother to child?
Objectives of the tutorial:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
nekrut
ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of the Estrogen receptor?
Objectives of the tutorial:
- Inspect read quality with FastQC
- Map reads with...
ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor
http://galaxyproject.github.io/training-material/topics/chip-seq/tutorials/estrogen-receptor-binding-site-identification/tutorial.html
http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-estrogen-receptor
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of the Estrogen receptor?
Objectives of the tutorial:
- Inspect read quality with FastQC
- Map reads with Bowtie2
- Assess the quality of an ChIP-seq experiments
- Extract coverage files
- Call enriched regions or peaks
friedue
erxleben
bebatut
vivekbhr
fidelram
Assembly - Unicycler Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - Unicycler Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html
http://tess.elixir-uk.org/materials/assembly-unicycler-assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- I have short reads and long reads. How do I assemble a genome?
Objectives of the tutorial:
- Perform Quality Control on your reads
- Perform a Small genome Assembly with Unicycler
- Evaluate the Quality of the Assembly with Quast
- Annotate the assembly with Prokka
nekrut
delphine-l
slugger70
Transcriptomics - Visualization of RNA-Seq results with CummeRbund
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select our desired subjects for differential gene expression analysis?
Objectives of the tutorial:
- Manage RNA-Seq...
Transcriptomics - Visualization of RNA-Seq results with CummeRbund
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-visualization-of-rna-seq-results-with-cummerbund
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select our desired subjects for differential gene expression analysis?
Objectives of the tutorial:
- Manage RNA-Seq results
- Extract the desired subject for differential gene expression analysis
- Visualize information
bagnacan
Proteomics - Peptide and Protein ID using OpenMS tools
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
Proteomics - Peptide and Protein ID using OpenMS tools
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-oms/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id-using-openms-tools
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
stortebecker
bgruening
Variant Analysis - Exome sequencing data analysis
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How to identify the genetic variation with the use of exome sequencing?
- What is the pipeline of the process of finding genetic variation which caused the disease?
Objectives of the...
Variant Analysis - Exome sequencing data analysis
http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html
http://tess.elixir-uk.org/materials/variant-analysis-exome-sequencing-data-analysis
Exome sequencing means that all protein-coding genes in a genome are sequenced
Questions of the tutorial:
- How to identify the genetic variation with the use of exome sequencing?
- What is the pipeline of the process of finding genetic variation which caused the disease?
Objectives of the tutorial:
- Identification of the genetic variation using the exome sequencing
- Using FreeBayes calls for variants generating
- Variant analysis and GEMINI queries
bebatut
torhou
erxleben
bgruening
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of Tal1?
- Which genes are regulated by Tal1?
Objectives of the tutorial:
- Inspect read quality with FastQC
-...
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
http://galaxyproject.github.io/training-material/topics/chip-seq/tutorials/tal1-binding-site-identification/tutorial.html
http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of Tal1?
- Which genes are regulated by Tal1?
Objectives of the tutorial:
- Inspect read quality with FastQC
- Perform read trimming with Trimmomatic
- Align trimmed reads with BWA
- Assess quality and reproducibility of experiments
- Identify Tal1 binding sites with MACS2
- Determine unique/common Tal1 binding sites from G1E and Megakaryocytes
- Identify unique/common Tal1 peaks occupying gene promoters
- Visually inspect Tal1 peaks with Trackster
malloryfreeberg
moheydarian
vivekbhr
joachimwolff
erxleben
Assembly - De Bruijn Graph Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - De Bruijn Graph Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html
http://tess.elixir-uk.org/materials/assembly-de-bruijn-graph-assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- What are the factors that affect genome assembly?
- How does Genome assembly work?
Objectives of the tutorial:
- Perform an optimised Velvet assembly with the Velvet Optimiser
- Compare this assembly with those we did in the basic tutorial
- Perform an assembly using the SPAdes assembler.
slugger70
Assembly - Introduction to Genome Assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...
Assembly - Introduction to Genome Assembly
http://galaxyproject.github.io/training-material/topics/assembly/tutorials/general-introduction/tutorial.html
http://tess.elixir-uk.org/materials/assembly-introduction-to-genome-assembly
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.
Questions of the tutorial:
- How do we perform a very basic genome assembly from short read data?
Objectives of the tutorial:
- assemble some paired end reads using Velvet
- examine the output of the assembly.
slugger70
Introduction to Galaxy Analyses - From peaks to genes
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Questions of the tutorial:
- How to use Galaxy?
- How to get...
Introduction to Galaxy Analyses - From peaks to genes
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html
http://tess.elixir-uk.org/materials/galaxy-introduction-from-peaks-to-genes
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Questions of the tutorial:
- How to use Galaxy?
- How to get from peak regions to a list of gene names?
Objectives of the tutorial:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how histories work
- Learn how to create a workflow
- Learn how to share your work
pajanne
blankclemens
bebatut
bgruening
nsoranzo
dyusuf
Epigenetics - DNA Methylation data analysis
DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
Questions of the tutorial:
- What is methylation and why it cannot be...
Epigenetics - DNA Methylation data analysis
http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html
http://tess.elixir-uk.org/materials/epigenetics-dna-methylation-data-analysis
DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
Questions of the tutorial:
- What is methylation and why it cannot be recognised by a normal NGS procedure?
- Can a different methylation influence the expression of a gene? How?
- Which tools you can use to analyse methylation data?
Objectives of the tutorial:
- Learn how to analyse methylation data
- Get a first intuition what are common pitfalls.
joachimwolff
dpryan79
Transcriptomics - Differential abundance testing of small RNAs
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What small RNAs are expressed?
- What RNA features have significantly different numbers of small RNAs targeting them between two conditions?
Objectives of the tutorial:
- Process small RNA-seq datasets...
Transcriptomics - Differential abundance testing of small RNAs
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/srna/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-differential-abundance-testing-of-small-rnas
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What small RNAs are expressed?
- What RNA features have significantly different numbers of small RNAs targeting them between two conditions?
Objectives of the tutorial:
- Process small RNA-seq datasets to determine quality and reproducibility.
- Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets.
- Differentiate between subclasses of small RNAs based on their characteristics.
- Identify differently abundant small RNAs and their targets.
malloryfreeberg
Transcriptomics - Reference-based RNA-Seq data analysis
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What are the effects of Pasilla (PS) gene depletion on splicing events?
- How to analyze RNA sequencing data using a reference genome?
Objectives of the tutorial:
- Analysis of RNA sequencing data using...
Transcriptomics - Reference-based RNA-Seq data analysis
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-reference-based-rna-seq-data-analysis
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What are the effects of Pasilla (PS) gene depletion on splicing events?
- How to analyze RNA sequencing data using a reference genome?
Objectives of the tutorial:
- Analysis of RNA sequencing data using a reference genome
- Analysis of differentially expressed genes
- Identification of functional enrichment among differentially expressed genes
bebatut
malloryfreeberg
moheydarian
erxleben
pavanvidem
blankclemens
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What genes are differentially expressed between G1E cells and megakaryocytes?
- How can we generate a transcriptome de novo from RNA sequencing data?
Objectives of the tutorial:
- Analysis of RNA...
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html
http://tess.elixir-uk.org/materials/transcriptomics-de-novo-transcriptome-reconstruction-with-rna-seq
Training material for all kinds of transcriptomics analysis.
Questions of the tutorial:
- What genes are differentially expressed between G1E cells and megakaryocytes?
- How can we generate a transcriptome de novo from RNA sequencing data?
Objectives of the tutorial:
- Analysis of RNA sequencing data using a reference genome
- Reconstruction of transcripts without reference transcriptome (de novo)
- Analysis of differentially expressed genes
malloryfreeberg
moheydarian
Metagenomics - Analyses of metagenomics data - The global picture
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- How to analyze metagenomics data?
- What information can be extracted of metagenomics data?
- What is the difference between amplicon and shotgun data?
- What are the difference...
Metagenomics - Analyses of metagenomics data - The global picture
http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html
http://tess.elixir-uk.org/materials/metagenomics-analyses-of-metagenomics-data-the-global-picture
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- How to analyze metagenomics data?
- What information can be extracted of metagenomics data?
- What is the difference between amplicon and shotgun data?
- What are the difference in the analyses of amplicon and shotgun data?
Objectives of the tutorial:
- Choosing the best approach to analyze metagenomics data
- Selection of tools to analyze amplicon data or shotgun data
- Visualisation of a community structure
shiltemann
bebatut
Metagenomics - 16S Microbial Analysis with Mothur
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- What is the effect of normal variation in the gut microbiome on host health?
Objectives of the tutorial:
- Analyze of 16S rRNA sequencing data using the Mothur toolsuite in...
Metagenomics - 16S Microbial Analysis with Mothur
http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
http://tess.elixir-uk.org/materials/metagenomics-16s-microbial-analysis-with-mothur
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Questions of the tutorial:
- What is the effect of normal variation in the gut microbiome on host health?
Objectives of the tutorial:
- Analyze of 16S rRNA sequencing data using the Mothur toolsuite in Galaxy
shiltemann
bebatut
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?
Objectives of the tutorial:
- MS1 feature...
Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-quant-sil/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-quantification-via-stable-isotope-labelling-sil
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?
Objectives of the tutorial:
- MS1 feature quantitation and mapping of quantitations to peptide and protein IDs.
stortebecker
bgruening
Proteomics - Secretome Prediction
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?
Objectives of the tutorial:
- Predict proteins in the cellular secretome by using...
Proteomics - Secretome Prediction
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/secretome-prediction/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-secretome-prediction
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?
Objectives of the tutorial:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by using WolfPSORT.
- Combine the results of both predictions.
stortebecker
bgruening
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-peptide-and-protein-id
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?
Objectives of the tutorial:
- Protein identification from LC-MS/MS raw files.
stortebecker
bgruening
Proteomics - Metaproteomics tutorial
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
- How can I perform taxonomy analysis and visualize metaproteomics data?
- How can I perform...
Proteomics - Metaproteomics tutorial
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html
http://tess.elixir-uk.org/materials/proteomics-metaproteomics-tutorial
Training material for proteomics workflows in Galaxy
Questions of the tutorial:
- How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
- How can I perform taxonomy analysis and visualize metaproteomics data?
- How can I perform functional analysis on this metaproteomics data?
Objectives of the tutorial:
- A taxonomy and functional analysis of metaproteomic mass spectrometry data.
timothygriffin
pratikdjagtap
jj-umn
blankclemens
Sequence analysis - RAD-Seq to construct genetic maps
Analyses of sequences
Questions of the tutorial:
- How to analyze RAD sequencing data for a genetic map study?
Objectives of the tutorial:
- SNP calling from RAD sequencing data
- Find and correct haplotypes
- Create input files for genetic map building software
Sequence analysis - RAD-Seq to construct genetic maps
http://galaxyproject.github.io/training-material/topics/sequence-analysis/tutorials/genetic-map-rad-seq/tutorial.html
http://tess.elixir-uk.org/materials/analysis-of-sequences-rad-seq-to-construct-genetic-maps
Analyses of sequences
Questions of the tutorial:
- How to analyze RAD sequencing data for a genetic map study?
Objectives of the tutorial:
- SNP calling from RAD sequencing data
- Find and correct haplotypes
- Create input files for genetic map building software
yvanlebras
Sequence analysis - RAD-Seq de-novo data analysis
Analyses of sequences
Questions of the tutorial:
- How to analyze RAD sequencing data without a reference genome for a population genomics study?
Objectives of the tutorial:
- Analysis of RAD sequencing data without a reference genome
- SNP calling from RAD sequencing data
- Calculate...
Sequence analysis - RAD-Seq de-novo data analysis
http://galaxyproject.github.io/training-material/topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial.html
http://tess.elixir-uk.org/materials/analysis-of-sequences-rad-seq-de-novo-data-analysis
Analyses of sequences
Questions of the tutorial:
- How to analyze RAD sequencing data without a reference genome for a population genomics study?
Objectives of the tutorial:
- Analysis of RAD sequencing data without a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics statistics from RAD sequencing data
yvanlebras
