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SidSin0809/README.md

Hello, I’m Siddharth Singh

Bio-data scientist | Multi-omics pipeline architect | Computational microbiome neurobiologist

I build fault-tolerant, production-ready pipelines that turn terabytes of raw omics data into testable biological insight. Recent work spans:

  • Streaming multi-GB+ HMDB XML files on low-RAM machines using Python iterparse and multithreading
  • Automating ligand preparation with Open Babel and AutoDockTools for structure-based drug discovery
  • Dissecting the molecular dialogue between the human microbiome and brain through Human Accelerated Regions (HARs)
  • Designing standardized, reproducible multi-omics workflows for large‐scale microbiome projects
  • Mapping metabolomic signatures that stratify COVID-19 severity
  • Using Mendelian randomization to link host genetics, gut microbes, and neuro-psychiatric risk

Core Competencies

Category Toolkit
Languages Python 3 (asyncio, pandas), R (tidyverse), Bash/Batch
Data Engineering multiprocessing, xml.etree.ElementTree, Airflow
Bio-/Cheminformatics HMDB, Open Babel, AutoDock Vina, PDB
Multi-omics Analytics MetaboAnalystR, NMDC EDGE, Cytoscape
Statistics Mendelian Randomization, multivariate metabolomics

Full list → Professional portfolio

🤝 Collaboration & Contact

  • I’m keen to collaborate on multi-omics standardization, resource-constrained bio-computing, and translational microbiome research.*
Channel Handle
Email mscphd2301171011@iiti.ac.in
LinkedIn /in/sidsin0809
ORCID 0000-0002-1388-6221

⚡ Fun Fact

When I’m not wrangling cells and code, you’ll find me sketching data-driven sci-fi storyboards.

Popular repositories Loading

  1. hmdb_endogenous_animal hmdb_endogenous_animal Public

    Fault-tolerant streaming crawler for HMDB Endogenous/Animal flags

    Python

  2. ligand_pdb2pdbqt ligand_pdb2pdbqt Public

    Automated Windows pipeline that protonates ligand PDB files at pH 7.4 and converts them in bulk to AutoDock-ready PDBQT format using Open Babel 3 + MGLTools

    Batchfile

  3. receptor-peptide-interface-mapper receptor-peptide-interface-mapper Public

    High-throughput identification of receptor–peptide contact residues from PDB/mmCIF structures (Python 3, Biopython, multithreaded)

    Python

  4. SidSin0809 SidSin0809 Public

    Config files for my GitHub profile.

  5. hmdb-endo-flagger hmdb-endo-flagger Public

    A Python toolkit to identify and score endogenous human metabolites from HMDB XML metadata

    Python

  6. hdock_batch hdock_batch Public

    Python utility that bulk-submits receptor/ligand pairs to the HDOCK server, tracks job tokens

    Python