Simon Bray

Former Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Topic: Computational chemistry

Tutorials

• Development in Galaxy / Contributing to BioBlend as a developer ✍️ 🧐
• Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
• Visualisation / Genomic Data Visualisation with JBrowse 🧐
• Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) 🧐
• Genome Annotation / Genome annotation with Funannotate 🧐
• Genome Annotation / Masking repeats with RepeatMasker 🧐
• Sequence analysis / Quality Control 🧐
• Statistics and machine learning / Regression in Machine Learning ✍️
• Statistics and machine learning / Classification in Machine Learning ✍️ 🧐
• Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring ✍️ 🧐
• Computational chemistry / Setting up molecular systems ✍️ 🧐
• Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib ✍️ 🧐
• Computational chemistry / Running molecular dynamics simulations using NAMD ✍️ 🧐
• Computational chemistry / High Throughput Molecular Dynamics and Analysis ✍️ 🧐
• Computational chemistry / Data management in Medicinal Chemistry 🧐
• Computational chemistry / Analysis of molecular dynamics simulations ✍️ 🧐
• Computational chemistry / Running molecular dynamics simulations using GROMACS ✍️ 🧐
• Computational chemistry / Protein-ligand docking ✍️ 🧐
• Single Cell / Single-cell quality control with scater 🧐
• Single Cell / Pre-processing of Single-Cell RNA Data 🧐
• Single Cell / Downstream Single-cell RNA analysis with RaceID 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis 🧐
• Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line ✍️
• Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes 🧐
• Metabolomics / Mass spectrometry imaging: Finding differential analytes 🧐
• Single Cell / Filtrado, representación y exploración de secuenciación de ARN de células únicas 🧐

Slides

• Genome Annotation / Introduction to Genome Annotation 🧐
• Statistics and machine learning / Convolutional neural networks (CNN) Deep Learning - Part 3 🧐
• Metabolomics / Introduction to Metabolomics 🧐

FAQs

• Creating a new file

Video Recordings

• Computational chemistry / High Throughput Molecular Dynamics and Analysis 💬 🗣
• Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line 💬 🗣
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 💬

GitHub Activity

github Issues Reported

24 Merged Pull Requests

See all of the github Pull Requests and github Commits by Simon Bray.

• Change default job runner to slurm in "Connecting Galaxy to a compute cluster tutorial"
• Fix link to advanced mdanalysis workflow
• Clarification about the G5E ligand in the HTMD tutorial
• Fix rendering of workflow import snippet
• Small updates / fixes for QC tutorial

Reviewed 26 PRs

We love our community reviewing each other's work!

• New tutorial: data management in medicinal chemistry
  computational-chemistry
• Add faq on creating workflow test
• Fix minor typos
• Update computational chemistry tutorial
• Fix rendering of workflow import snippet

News

External Links

Favourite Topics

Favourite Formats