Foundations of Bioinformatics and Computational Biology Training Program

Gain expertise in bioinformatics fundamentals, computational biology, and omics data interpretation through real-world practical sessions.

Foundations of Bioinformatics & Computational Biology

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Session Index

Session 1 — Unix, Data Formats & Reproducibility Session 2 — Algorithms: Similarity, Alignment & Scoring Session 3 — Gene Structures & Functional Annotation Session 4 — Mini Capstone: End-to-End Pipeline

Session 1

Fee: Rs 4500

Unix, Data Formats & Reproducibility

Linux shell essentials: grep, awk, sed pipelines

GNU coreutils grep awk sed bash tmux

File integrity: checksum & metadata management

sha256sum md5sum exiftool rsync

Core bioinformatics formats: FASTA, FASTQ, GFF3, BED, VCF

Theory

Programmatic data retrieval from NCBI/EBI/UniProt

NCBI EDirect Entrez (Biopython) wget curl

Environment isolation using Conda

Conda Mamba Micromamba

Jupyter reproducible notebook setup

JupyterLab nbconvert Papermill Python

Session 2

Fee: Rs 6000

Algorithms: Similarity, Alignment & Scoring

Needleman–Wunsch vs Smith–Waterman alignment comparison

Theory

PAM/BLOSUM matrix handling and interpretation

Theory

Local BLAST setup & custom database building

NCBI BLAST+ makeblastdb DIAMOND

Multiple sequence alignment (Clustal Omega, MUSCLE)

Clustal Omega MUSCLE MAFFT

Format conversions and consensus generation

seqkit seqtk EMBOSS seqret EMBOSS cons

Automated batch alignment reporting

Biopython pandas matplotlib

Session 3

Fee: Rs 8000

Gene Structures & Functional Annotation

ORF detection and annotation using Prodigal

Prodigal EMBOSS getorf

Functional domain mapping with InterProScan

InterProScan HMMER3 Pfam

Annotation transfer and evidence scoring

DIAMOND BLAST+ Prokka eggNOG-mapper

Parsing and formatting GFF3/BED files

bedtools gffread BCBio.GFF

Quality checks for codon usage & frameshifts

EMBOSS cusp CodonW FrameDP

Preparing summary annotation reports

pandas JupyterLab R Markdown/Quarto

Session 4

Fee: Rs 10000

Mini Capstone: End-to-End Pipeline

Designing complete analysis workflow

Theory

Data import, QC, alignment & annotation automation

Snakemake FastQC MultiQC BLAST+ Prodigal

Snakemake pipeline setup for reproducibility

Snakemake Git Conda/Mamba

Containerization with Docker

Docker CE Podman Apptainer/Singularity

Final report preparation and defense

Quarto JupyterLab pandas

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Foundations of Bioinformatics & Computational Biology Training | NTHRYS Hyderabad | Bangalore | Chennai | Kochi | Dallas - US

Foundations of Bioinformatics and Computational Biology Training Program