Simon Bray
Former Affiliations
UFR
ELIXIR EuropeContributions
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
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) 🧐
- Genome Annotation / Genome annotation with Funannotate 🧐
- Genome Annotation / Masking repeats with RepeatMasker 🧐
- Statistics and machine learning / Regression in Machine Learning ✍️
- Statistics and machine learning / Classification in Machine Learning ✍️ 🧐
- Transcriptomics / Reference-based RNA-Seq data analysis 🧐
- Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line ✍️
- Development in Galaxy / Contributing to BioBlend as a developer ✍️ 🧐
- Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes 🧐
- Metabolomics / Mass spectrometry imaging: Finding differential analytes 🧐
- Visualisation / Genomic Data Visualisation with JBrowse 🧐
- Sequence analysis / Quality Control 🧐
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
- Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
- Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
- Computational chemistry / High Throughput Molecular Dynamics and Analysis ✍️ 🧐
- Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib ✍️ 🧐
- Computational chemistry / Data management in Medicinal Chemistry 🧐
- Computational chemistry / Setting up molecular systems ✍️ 🧐
- Computational chemistry / Protein-ligand docking ✍️ 🧐
- Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring ✍️ 🧐
- Computational chemistry / Running molecular dynamics simulations using NAMD ✍️ 🧐
- Computational chemistry / Running molecular dynamics simulations using GROMACS ✍️ 🧐
- Computational chemistry / Analysis of molecular dynamics simulations ✍️ 🧐
- Single Cell / Downstream Single-cell RNA analysis with RaceID 🧐
- Single Cell / Pre-processing of Single-Cell RNA Data 🧐
- Single Cell / Single-cell quality control with scater 🧐
Slides
- Genome Annotation / Introduction to Genome Annotation 🧐
- Statistics and machine learning / Convolutional neural networks (CNN) Deep Learning - Part 3 🧐
- Metabolomics / Introduction to Metabolomics 🧐
FAQs
- Erstellen einer neuen Datei ✍️
- Creating a new file
- Creación de un nuevo fichero ✍️
- Get the workflow id
Video Recordings
- Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line 💬 🗣
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 💬
- Computational chemistry / High Throughput Molecular Dynamics and Analysis 💬 🗣
GitHub Activity
github Issues Reported
24 Merged Pull Requests
See all of the github Pull Requests and github Commits by Simon Bray.
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Change default job runner to slurm in "Connecting Galaxy to a compute cluster tutorial"
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Fix link to advanced mdanalysis workflow
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Clarification about the G5E ligand in the HTMD tutorial
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Fix rendering of workflow import snippet
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Small updates / fixes for QC tutorial
Reviewed 27 PRs
We love our community reviewing each other's work!
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Update tutorial.md
computational-chemistry -
New tutorial: data management in medicinal chemistry
computational-chemistry -
Add faq on creating workflow test
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Fix minor typos
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Update computational chemistry tutorial
