• Carpentree test case

    Manual example created as proof of concept for our Carpentree project, created at the #CollabW19 workshop in Loughborough on 3 April 2019

    The lessons referred to are:
    - Programming with Python (PP): http://swcarpentry.github.io/python-novice-inflammation/index.html
    - Plotting and...

  • ChIP-seq workflow

    Basic workflow for ChIP-seq analysis

    Topic: ChIP-seq

  • ChIP-seq workflow (with intermediate data)

    Basic workflow for ChIP-seq analysis

    Topic: ChIP-seq

  • ChIP-seq workflow in Bioconductor

    Basic workflow for ChIP-seq analysis using Bioconductor from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389943/

    Topic: ChIP-seq

  • EBI metagenomics pipeline 2.0

    EBI metagenomics pipeline 2.0

  • ELIXIR Structural Bioinformatics 1: Getting a structure for a protein of interest

    This training workflow is designed to lead you through the process of finding experimentally-determined structures for a protein you are interested in - or predicting structure information if one is not available.

    It will then help guide you through visualising that structure as a prerequisite...

  • ELIXIR Structural Bioinformatics 2: Exploring protein domains and functional sites

    This training workflow introduces how to search (using query protein sequences or structures) for protein domains, conservation and protein family information, surface and topological interfaces, and possible ligand binding sites.

    It is designed to lead you through the process of finding...

  • ELIXIR Structural Bioinformatics 3: Predicting the effect of mutation on protein function

    This workflow builds on the previous training workflows in this series on building protein models and identifying functional domains or ligand binding sites - and introduces methods to predict how mutations can impact on protein function.

    It is designed to lead you through the process of...

  • EMBER: A practical guide to Bioinformatics

    This practical introduces a range of Web-based databases and tools, allowing their relative strengths and weaknesses to be compared. The practical comprises several modules, each broken down into simple steps.

  • Homology Modelling with SWISS-MODEL

    This is the workflow of homology modelling with the SWISS-MODEL expert system

    SWISS-MODEL is a web-based integrated service dedicated to protein structure homology modelling. It guides the user in building protein homology models at [different levels of...

  • Image analysis

    Imaging (http://edamontology.org/topic_3382)

    Bioimage informatics (EDAM-bioimaging)

  • Meta-pipe


  • Multiple Sequence Alignment, Analysis and Figure Generation with Jalview

    This workflow accompanies a methods in molecular biology chapter currently in preparation.

  • Peroxisomal Proteins Detection

    Workflow to identify putative peroxisomal proteins from the FASTA sequence

  • Phylogeny.fr "One Click" phylogeny

    Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.
    Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.

    The "one click"...

  • Protein Structure Modelling

    This is the a workflow of protein modelling.

  • READemption

    READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples. Meanwhile is has been extended to process data generated in different...

  • RNA-seq summarization with annotated genome

    Basic workflow for RNA-seq analysis to get to a count table.

  • Structural bioinformatics workflow

    A workflow with suggested common stages taken in structural bioinformatics

  • Text mining and annotation

    Natural language processing (http://edamontology.org/topic_0218)

  • Text mining and annotation (more detail)

    Natural language processing (http://edamontology.org/topic_0218)

  • Training course in Transcriptomics

    Workflow for Transcirptomics course for CABANA learning

  • TRUFA RNAseq

    TRUFA (Transcriptomes User-Friendly Analysis) is a free webserver designed to help you perform RNA-seq analysis.

    So far, TRUFA is allowing you to execute the following steps (programs used are specified in the parentheses):

    Reads cleaning:
    Reads quality control (FASTQC)
    Quality trimming...