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.

• Proteomics
• Clinical metaproteomics workflows within Galaxy
• Proteogenomics

Tutorials

• Proteomics / Clinical Metaproteomics 5: Data Interpretation ✍️ 🧐
• Proteomics / Proteogenomics 1: Database Creation ✍️ 🧐
• Proteomics / Neoantigen 6: Predicting HLA Binding ✍️
• Proteomics / Clinical Metaproteomics 4: Quantitation ✍️ 🧐
• Proteomics / Peptide Library Data Analysis 🧐
• Proteomics / Neoantigen 1: Fusion-Database-Generation ✍️
• Proteomics / metaQuantome 2: Function ✍️ 🧐
• Proteomics / DIA Analysis using OpenSwathWorkflow 🧐
• Proteomics / Clinical Metaproteomics 1: Database-Generation ✍️ 🧐
• Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
• Proteomics / Clinical Metaproteomics 2: Discovery ✍️ 🧐
• Proteomics / EncyclopeDIA ✍️ 🧐
• Proteomics / Clinical Metaproteomics 3: Verification ✍️ 🧐
• Proteomics / Neoantigen 5: Variant Annotation ✍️
• Proteomics / Machine Learning Modeling of Anticancer Peptides 🧐
• Proteomics / Proteogenomics 2: Database Search ✍️ 🧐
• Proteomics / Proteogenomics 3: Novel peptide analysis ✍️ 🧐
• Proteomics / Neoantigen 2: Non-Reference-Database-Generation ✍️
• Proteomics / Neoantigen 3: Database merge and FragPipe discovery ✍️
• Proteomics / metaQuantome 1: Data creation ✍️ 🧐
• Proteomics / Metaproteomics tutorial ✍️ 🧐
• Proteomics / Neoantigen 7: IEDB binding PepQuery Validated Neopeptides ✍️
• Proteomics / Neoantigen 4: PepQuery2 Verification ✍️
• Proteomics / metaQuantome 3: Taxonomy ✍️ 🧐
• Proteomics / Statistical analysis of DIA data 🧐
• Proteomics / Library Generation for DIA Analysis 🧐
• 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 2024 🧑‍🏫

GitHub Activity

github Issues Reported

44 Merged Pull Requests

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

• edited the typo
  proteomics
• Update Clinical metaproteomics tutorials
  proteomics
• Update main_workflow.ga
  proteomics
• Created a learning pathway for GTA- proteogenomics.md
  template-and-tools
  proteomics
• Adding Video recordings to the tutorials
  template-and-tools
  proteomics

Reviewed 19 PRs

We love our community reviewing each other's work!

• github Add missing data-library.yaml files
  proteomics
• Update main_workflow.ga
  proteomics
• Adding Video recordings to the tutorials
  template-and-tools
  proteomics
• created 5 clinical metaproteomics tutorials
  template-and-tools
  proteomics
• fix a broken box

External Links

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