School of Bioinformatics · Foundations
Bioinformatics Foundations
A first course for life-science students and researchers who want to work with biological data rather than only read about it: what each kind of data measures, where it is kept, how to read it and how to run the standard tools on it.
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Course overview
Bioinformatics Foundations is the entry point to the catalogue. It covers the data types that modern biology produces, the public databases where those data are kept, the file formats that every downstream tool expects, and the command-line environment in which most analysis is done.
The emphasis is on reading data correctly before analysing it: what a FASTQ quality string encodes, why a BLAST E-value depends on the size of the database, how coordinates differ between BED and GFF. Each module ends with a lab on real records from NCBI, Ensembl, UniProt or the Protein Data Bank, and the course closes with a short annotation project written up as a report.
Learning outcomes
By the end of the course you will be able to:
- Explain what sequencing, expression and structure data measure, and their typical sources of error
- Find, download and cite records from NCBI, Ensembl, UniProt and the PDB
- Read and validate FASTA, FASTQ, SAM/BAM, VCF, BED and GFF files
- Run BLAST and pairwise alignments, and interpret scores and E-values
- Work in the Linux command line and organise a reproducible project folder
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Undergraduate-level molecular biology
- No programming experience required
Best suited to
- B.Sc., M.Sc. and B.Tech. students in biology, biotechnology, microbiology or pharmacy
- Wet-lab researchers who want to analyse their own data
- Anyone preparing for a specialised bioinformatics course or internship
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- The central dogma from a data point of view
- What a sequencer, an array and a mass spectrometer report
- Reference genomes, annotation releases and versions
Topics
- NCBI, Ensembl, UniProt and the PDB
- Accessions, identifiers and ID mapping
- Citing data and respecting licences
Topics
- FASTA and FASTQ; Phred quality scores
- SAM/BAM, VCF, BED and GFF/GTF
- Validating and converting files
Topics
- Scoring matrices and gap penalties
- Global versus local alignment
- BLAST: E-values, bit scores and common pitfalls
Topics
- Navigating the file system; pipes and redirection
- grep, awk, sort and uniq on biological files
- Installing tools with conda
Topics
- From raw sequence to identity and function
- Documenting every step
- Writing a short report
Practical sessions and projects
Capstone project
Annotate an unknown gene
Start from an unlabelled sequence, identify it, find its protein, structure and known variants, and write up the evidence trail so that a reader could repeat every step.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Biology as data
Follow one human gene (HBB) from genome coordinates to transcript, protein and structure records, noting the identifier each database uses.
- Biological databases
Retrieve sequences and metadata programmatically with NCBI E-utilities and the Ensembl REST API, and convert between identifier systems.
- File formats
Inspect real FASTQ, SAM and VCF files, decode a Phred quality string by hand and repair a deliberately broken FASTA file.
- Sequence alignment
Run BLASTN and BLASTP searches, compare global and local alignments of the same pair, and show how the E-value changes with database size.
- The command line
Build a one-line pipeline that summarises the E. coli GFF annotation by feature type and strand.
- Project: annotate an unknown gene
Identify an unlabelled sequence and trace it to its protein, structure and known variants in a two-page report with an evidence trail.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Human β-globin (HBB) records: Following one gene across databases.NCBI RefSeq, Ensembl, UniProt P68871, PDB
- Escherichia coli K-12 MG1655 genome and annotation: Command-line work on a real genome and GFF file.NCBI RefSeq NC_000913.3
- HIV-1 protease with a bound inhibitor: Reading a structure entry: resolution, chains and ligands.RCSB PDB entry 1HSG
Core reading
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. Journal of Molecular Biology 215:403–410.
- Shotts W. The Linux Command Line, 2nd edition. No Starch Press, 2019.
- NCBI Handbook and the Ensembl, UniProt and RCSB PDB documentation (online).
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Bioinformatics Foundations, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Bioinformatics Foundations
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
Yes. The command line is taught from the first command, and no programming is assumed. Programming in Python or R is the next step on every learning path.
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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