Subina Mehta

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: Proteomics
• Learning Pathway: Clinical metaproteomics workflows within Galaxy
• Learning Pathway: Neoantigen discovery using the iPepGen pipeline
• Learning Pathway: Proteogenomics

Tutorials

• Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
• Proteomics / Proteogenomics 3: Novel peptide analysis ✍️ 🧐
• Proteomics / Label-free data analysis using MaxQuant 🧐
• Proteomics / Neoantigen 5b: IEDB binding Validated Neopeptides ✍️ 🧐
• Proteomics / Statistical analysis of DIA data 🧐
• Proteomics / metaQuantome 2: Function ✍️ 🧐
• Proteomics / metaQuantome 1: Data creation ✍️ 🧐
• Proteomics / Neoantigen 3: PepQuery2 Verification ✍️ 🧐
• Proteomics / Clinical Metaproteomics 4: Quantitation ✍️ 🧐
• Proteomics / Metaproteomics tutorial ✍️ 🧐
• Proteomics / Peptide Library Data Analysis 🧐
• Proteomics / Clinical Metaproteomics 2: Discovery ✍️ 🧐
• Proteomics / Clinical Metaproteomics 3: Verification ✍️ 🧐
• Proteomics / Proteogenomics 2: Database Search ✍️ 🧐
• Proteomics / Neoantigen 4: Variant Annotation ✍️ 🧐
• Proteomics / Proteogenomics 1: Database Creation ✍️ 🧐
• Proteomics / EncyclopeDIA ✍️ 🧐
• Proteomics / DIA Analysis using OpenSwathWorkflow 🧐
• Proteomics / Clinical Metaproteomics 5: Data Interpretation ✍️ 🧐
• Proteomics / Machine Learning Modeling of Anticancer Peptides 🧐
• Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
• Proteomics / metaQuantome 3: Taxonomy ✍️ 🧐
• Proteomics / Neoantigen 1b: Non-Reference-Database-Generation ✍️ 🧐
• Proteomics / Neoantigen 5a: Predicting HLA Binding ✍️ 🧐
• Proteomics / Neoantigen 1a: Fusion-Database-Generation ✍️ 🧐
• Proteomics / Library Generation for DIA Analysis 🧐
• Proteomics / Neoantigen 2: Database merge and FragPipe discovery ✍️ 🧐
• Proteomics / Clinical Metaproteomics 1: Database-Generation ✍️ 🧐
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) ✍️
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data ✍️

Slides

• Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
• Microbiome / Introduction to metatranscriptomics ✍️ 🧐

FAQs

• Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools?
• Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
• Why do we use FASTQ interlacer and not the FASTQ joiner?
• Can we use the ASaiM-MT workflow on multiple input files at the same time?
• In the MVP platform, is it possible to view the genomic location of all the peptides?
• Example histories for the proteogenomics tutorials
• Can I use these workflows on datasets generated from our laboratory?
• The workflows contain several Query tabular for text manipulation, is there a tutorial for that?
• What kind of variants are seen in the output?
• How many search engines can you use in SearchGUI?
• Can this ASaiM workflow be used for single-end data?
• Why do we have a variant mapping file when it is not being used in the workflow?
• Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?

Video Recordings

• Proteomics / Proteogenomics 3: Novel peptide analysis 💬 🗣
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) 🗣
• Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data 🗣

Events

• Galaxy Training Academy 2025 🧑‍🏫
• Galaxy Training Academy 2026 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

50 Merged Pull Requests

See all of the github Pull Requests and github Commits by Subina Mehta.

• Update tutorial.md with new unipept version for viewer changes
  proteomics
• Add files via upload
  template-and-tools
• Update tutorial.md
  proteomics
• Update neoantigen.md
  template-and-tools
• Update neoantigen.md
  template-and-tools

Reviewed 36 PRs

We love our community reviewing each other's work!

• Enhance tutorial with peptide annotation and queries
  proteomics
  faqs
• Refine neoantigen tutorial content and structure
  proteomics
• Enhance tutorial with genomic and variant annotation details
  proteomics
• Update neoantigen tutorials
  proteomics
• Introduce One-Click Neoantigen Workflow section
  template-and-tools

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