NEW | 🧬 Bioinformatics & Agri-Genomics Workshop
20 modules · 3 certifications
📍 New Delhi, India ✉️ krishigene@gmail.com
🌾 Certified Hybrid Seeds — Learn More 🧪 NABL Accredited Soil Testing — Results in 48 Hours 🎓 New Batch: Smart Farming Course Starts July 2026 🧬 Bioinformatics Workshop Series — Enroll Now 💰 PM Kisan Samman Nidhi — Check Eligibility 🚁 Drone Spraying Services Launched in 10+ States 🌱 Level 1 Bioinformatics — Beginner Batch Open 📊 Free Farm Analysis for New Members 🔬 Level 2 NGS & Transcriptomics — Join Now 👨‍🌾 Expert Advisory Sessions — Book Today 🌾 Certified Hybrid Seeds — Learn More 🧪 NABL Accredited Soil Testing — Results in 48 Hours 🎓 New Batch: Smart Farming Course Starts July 2026 🧬 Bioinformatics Workshop Series — Enroll Now 💰 PM Kisan Samman Nidhi — Check Eligibility 🚁 Drone Spraying Services Launched in 10+ States 🌱 Level 1 Bioinformatics — Beginner Batch Open 📊 Free Farm Analysis for New Members 🔬 Level 2 NGS & Transcriptomics — Join Now 👨‍🌾 Expert Advisory Sessions — Book Today
KrishiGene - Smart Farming
🌤️
Mausam / Weather
Suitable for Sowing
📊
Mitti / Soil
pH 6.8 — Uttam
🌱 India's Premier AgriTech Platform 2026

खेती को बनाएं स्मार्ट और लाभदायक

Make Farming Smart & Profitable with KrishiGene

बीज से लेकर बाजार तक — डिजिटल कृषि, विशेषज्ञ सलाह, सरकारी योजनाएं और सर्वोत्तम बीज व उर्वरक एक ही जगह।
From seed to market — digital farming, expert advisory, govt schemes, best seeds & fertilizers.

18L+
Farmers / किसान
32
States / राज्य
600+
Seed Varieties / बीज किस्में
250+
Agri Experts / विशेषज्ञ
🌱
बीज / Seeds
500+ किस्में
🧪
उर्वरक / Fertilizer
Best Prices
🏛️
सरकारी योजनाएं
Govt Schemes
🔬
मिट्टी जांच
Soil Testing ₹299
🎓
किसान प्रशिक्षण
Farmer Training
👨‍🌾
विशेषज्ञ सलाह
Expert Advisory
🌿
पौधा डेटाबेस
Plant Database
OUR SERVICES

Complete Agriculture Solutions

From farm analysis to market access — KrishiGene provides end-to-end solutions for every stage of your agricultural journey.

📊
Farm & Crop Analysis
Satellite imagery, NDVI mapping, soil health scoring, and AI-powered pest detection for precision farming.
Explore Service →
🌱
Seeds & Varieties
Certified, tested hybrid and open-pollinated seeds. 500+ varieties across 40+ crops.
Explore Service →
🧪
Lab Testing Services
NABL-accredited soil, water, foliar, and pesticide residue testing with 48-hour turnaround.
Explore Service →
📢
Agri Marketing
Reach 12L+ farmers through targeted digital campaigns, WhatsApp blasts, and regional language content.
Explore Service →
👨‍🌾
Expert Advisory
24/7 access to 200+ certified agronomists, plant pathologists, and crop doctors via call, chat, or video.
Explore Service →
🚁
Drone Services
Aerial surveying, precision spraying, and crop monitoring with DGCA-certified drone operators.
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💰
Agri Finance & Insurance
KCC loans, Fasal Bima, FPO financing, and microinsurance — complete financial solutions for farmers.
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💻
Farm Management Software
Digital khata, crop calendar, inventory management, and IoT integration for smart farming.
Explore Service →
🤝
Procurement & Trading
Direct farmer-to-buyer connect. FPO aggregation, MSP advisory, and market linkage services.
Explore Service →
🏆
NABL Accredited
Soil Lab Testing
🚁
DGCA Certified
Drone Operators
🌱
ICAR Approved
Certified Seeds
📱
24/7 Available
WhatsApp Support
🏛️
Govt Registered
Pvt. Ltd. Company
COURSES & WORKSHOPS

Upskill Your Farming

FARMER STORIES

What Our Farmers Say

★★★★★

"KrishiGene ki soil testing service se mujhe pata chala ki meri mitti mein zinc ki kami hai. Ab meri wheat ki yield 40% badh gayi hai!"

RK
Ramesh Kumar
📍 Muzaffarnagar, UP
★★★★★

"Drone spraying service bahut kaam aai. 10 acre ki spraying sirf 45 minute mein ho gayi aur kharcha bhi kam pada. Expert advisory team 24 ghante available rehti hai."

SP
Suresh Patel
📍 Anand, Gujarat
★★★★★

"Smart Farming course se mujhe drip irrigation aur fertigation ka poora knowledge mila. Ab mera FPO 500 members ka hai aur hum seedha market mein bechte hain."

PM
Priya Mehra
📍 Nashik, Maharashtra

Our Agriculture Services

End-to-end solutions for every stage of the farm-to-market journey

Courses & Workshops

Learn from India's best agri experts — online, field demonstrations, and certification programs

🧬 FLAGSHIP PROGRAM

Bioinformatics &
Agri-Genomics
Workshop Series

A structured 3-level training program — from foundational biology and computing to advanced AI, single-cell omics, and precision breeding. 20 modules. Full certifications.

🌱
Level 1 — Beginner
6 Modules · Linux, Python, R, Stats, Omics
🔬
Level 2 — Intermediate
6 Modules · NGS, RNA-seq, Metabolomics
🚀
Level 3 — Advanced
8 Modules · HPC, AI/ML, scRNA-seq
3
Certifications
4
Specialisations

Plant & Crop Database

Detailed information on 200+ crops — varieties, nutrition, pests, diseases, and management practices

🏛️ किसानों के लिए सरकारी योजनाएं

Government Schemes for Farmers — Eligibility, Benefits & How to Apply | केंद्र एवं राज्य सरकार की सभी योजनाओं की पूरी जानकारी

योजना में मदद चाहिए? / Need Help with Application?

KrishiGene की टीम किसी भी सरकारी योजना में आवेदन में मदद करती है। Our team helps you apply for any government scheme free of cost.

💬 WhatsApp Help

📰 KrishiGene Agri Blog 2026

Latest news, market updates, farming tips & government schemes in Hindi & English | खेती की ताज़ा जानकारी हिंदी और अंग्रेज़ी में

About KrishiGene

We are on a mission to digitise India's agriculture value chains — one cluster at a time

OUR STORY

Born from the Fields,
Built for Farmers

KrishiGene was founded with a singular vision: to harness the power of genomics, data, and digital technology to transform Indian agriculture. We believe every farmer deserves access to world-class agronomic intelligence.

Our platform integrates the best of biotechnology (the "Gene" in KrishiGene) with traditional farming wisdom (Krishi), creating solutions that are both cutting-edge and deeply rooted in India's agricultural reality.

2019
Year Founded
28
States Active

Our Values

🌱
Farmer First

Every decision starts with what's best for the farmer

🔬
Science-Backed

All recommendations grounded in peer-reviewed research

🤝
Community Driven

Building networks that lift entire farming communities

♻️
Sustainable Future

Promoting practices that protect the land for future generations

LEADERSHIP

Meet Our Team

Get In Touch

We're here to help — reach out to our team anytime

Send us a Message

📞 Contact Us

📞
KrishiGene Helpline +91 7982263854
Mon–Sat, 9am – 6pm
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Quick reply within 30 min
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📍 Office Addresses

Head Office — New DelhiRZ-G-10, FIRST FLOOR,KH NO 55/13,RAJ NAGAR PART-II, SOUTH WEST DELHI-110077 (DELHI)
R&D Centre — New DelhiNear Pusa Campus IARI NEW DELHI- 110012

💬 WhatsApp Support

Get instant help on WhatsApp — our team responds within 30 minutes during business hours

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Privacy Policy

How KrishiGene collects, uses, and protects your information

Last updated: July 2026

At KrishiGene Technologies Pvt. Ltd. ("KrishiGene", "we", "us", or "our"), your privacy is important to us. This Privacy Policy explains what information we collect, how we use it, and the choices you have. By using our website and services, you agree to the practices described here.

1. Information We Collect

We may collect the following information when you register, book a service, enroll in a course, or contact us:

  • Personal details such as your name, phone number, email address, and state.
  • The category you identify as (for example, farmer, dealer, FPO, student, or company).
  • Details of the services, courses, or advisory you request from us.
  • Messages and enquiries you send through our contact forms.
  • Basic technical data such as browser type and general usage information to improve the site.

2. How We Use Your Information

  • To create and manage your account and provide the services you request.
  • To respond to your enquiries and offer agricultural advisory and support.
  • To send you important updates about your registrations, courses, or bookings.
  • To share relevant information about government schemes, workshops, and services (you can opt out anytime).
  • To improve our platform, content, and customer experience.

3. Sharing of Information

We do not sell your personal information. We may share limited information only with trusted service partners who help us operate the platform (for example, communication or hosting providers), or where required by law. All such partners are expected to keep your information secure and use it only for the agreed purpose.

4. Data Security

We use reasonable technical and organisational measures to protect your information against unauthorised access, alteration, or disclosure. However, no method of transmission over the internet is completely secure, and we cannot guarantee absolute security.

5. Cookies

Our website may use cookies and similar technologies to remember your preferences and understand how the site is used. You can control cookies through your browser settings.

6. Your Rights

You may request access to, correction of, or deletion of your personal information by contacting us. You may also unsubscribe from promotional messages at any time.

7. Children's Privacy

Our services are intended for users aged 18 and above. We do not knowingly collect personal information from children.

8. Changes to This Policy

We may update this Privacy Policy from time to time. Any changes will be posted on this page with a revised "Last updated" date.

9. Contact Us

If you have any questions about this Privacy Policy, please contact us at krishigene@gmail.com or call +91 7982263854.

Terms of Service

The terms that govern your use of KrishiGene

Last updated: July 2026

These Terms of Service ("Terms") govern your access to and use of the KrishiGene website, services, courses, and content. By using our platform, you agree to these Terms. Please read them carefully.

1. Use of Our Services

You agree to use KrishiGene only for lawful purposes and in a way that does not infringe the rights of others. You are responsible for the accuracy of the information you provide during registration and while using our services.

2. Accounts

When you create an account, you are responsible for keeping your login details confidential and for all activity under your account. Please notify us immediately if you suspect any unauthorised use.

3. Services, Advisory & Courses

KrishiGene provides agricultural services, advisory, training courses, plant information, and details about government schemes. This information is provided for general guidance and educational purposes. While we strive for accuracy, results may vary based on local conditions, and our content should not replace professional or on-field expert judgement where required.

4. Fees & Enrolment

Certain courses or services may carry a fee, which will be clearly stated before you enrol or book. Any applicable fees, refunds, or cancellation terms will be communicated to you at the time of enrolment.

5. Intellectual Property

All content on this platform, including text, graphics, logos, and course material, is the property of KrishiGene or its licensors and is protected by applicable laws. You may not copy, reproduce, or distribute it without our written permission.

6. Third-Party Links

Our website may contain links to government portals and other third-party websites. We are not responsible for the content, policies, or practices of those websites.

7. Limitation of Liability

To the extent permitted by law, KrishiGene shall not be liable for any indirect or consequential loss arising from the use of, or inability to use, our platform or services.

8. Changes to These Terms

We may revise these Terms from time to time. Continued use of our platform after any change means you accept the updated Terms.

9. Governing Law

These Terms are governed by the laws of India. Any disputes shall be subject to the jurisdiction of the courts of New Delhi.

10. Contact Us

For any questions about these Terms, contact us at krishigene@gmail.com or call +91 7982263854.

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🧬 FLAGSHIP PROGRAM

Bioinformatics &
Agri-Genomics
Workshop Series

A comprehensive 3-level training program — from biological foundations to advanced AI, single-cell omics, and precision breeding. Designed for researchers, students, and agri-data scientists across India.

3
Skill Levels
20
Modules
400+
Hours of Training
4
Specialisations
CERTIFICATION PATHWAY

Three Levels, One Complete Journey

Progress at your pace — each level builds on the last, culminating in professional-grade bioinformatics capability

🌱
LEVEL 1

Beginner

Biological foundations, Linux, programming, statistics and basic omics analysis

6 Modules + Capstone ~180 hours
Earns: Bioinformatics Analyst Certificate
POPULAR
🔬
LEVEL 2

Intermediate

NGS, transcriptomics, metabolomics, functional genomics and comparative analysis

6 Modules + Capstone ~180 hours
Earns: Omics Data Scientist Certificate
🚀
LEVEL 3

Advanced / Professional

HPC, AI/ML, single-cell omics, structural bioinformatics and industry applications

8 Modules + Capstone ~240 hours
Earns: Computational Biologist Certificate
SPECIALISATION TRACKS

Choose Your Focus Area

After completing the core curriculum, specialise in one of four tracks aligned to your career goals

🌱

Plant Bioinformatics

Pan-genomics, crop GWAS, stress tolerance genomics, genomic selection for breeding programs

Pan-Genomics Crop GWAS Genomic Selection
🏥

Medical Bioinformatics

Clinical genomics, precision medicine, pharmacogenomics, variant interpretation (ACMG)

Clinical Genomics Pharmacogenomics Variant Calling
🤖

AI-Driven Bioinformatics

Deep learning for sequence analysis, AlphaFold, biomarker discovery, gene expression prediction

Deep Learning AlphaFold Biomarker Discovery
🔗

Multi-Omics Systems Biology

Systems-level integration, GRN inference, flux balance analysis, multi-omics factor analysis

MOFA+ GRN Inference FBA

Who Is This Program For?

🎓

Students & Researchers

BSc/MSc/PhD students in biology, botany, biochemistry, genetics, or computer science seeking bioinformatics skills

🌾

Agri Professionals

Plant breeders, agronomists, and seed company professionals wanting to integrate genomics into their work

💻

Data Scientists

Software engineers and data scientists transitioning into bioinformatics, computational biology, or health data science

Ready to Start Your Bioinformatics Journey?

Join researchers and students from across India. Learn at your own pace with expert mentorship.

🌱 LEVEL 1

Beginner Bioinformatics

Build strong foundations in biology, computing, statistics, and basic omics analysis.

6
Modules
190h
Total Hours
4
Capstone Options

6 Modules — Full Curriculum

Click any module to see full details, tools, practicals and learning outcomes

🧬
MODULE 1
Biological Foundations

Central Dogma, Genetics & Genomic Databases

Central Dogma of Molecular BiologyDNA / RNA / Protein structureGene Expression & RegulationChromosomes & Genome Organisation
NCBI EntrezEnsembl BrowserUniProtExPASy
⏱ 3 weeks · 30 hrs View Details →
🖥️
MODULE 2
Linux & Command Line

Bash, Shell Scripting & Remote Server Mastery

Linux File System & NavigationBash Commands & ShortcutsFile Permissions & OwnershipText Processing & Regex
grepawksedtmux
⏱ 3 weeks · 30 hrs View Details →
🐍
MODULE 3
Programming for Bioinformatics

Python & R for Biological Data Science

Python: Variables, Loops, FunctionsPython: Pandas, NumPy, BiopythonPython: File I/O & Sequence ParsingPython: Data Visualisation (Matplotlib, Seaborn)
Python 3BiopythonPandasR 4.x
⏱ 4 weeks · 40 hrs View Details →
📊
MODULE 4
Statistics for Bioinformatics

Hypothesis Testing, PCA & Multiple Testing

Probability DistributionsHypothesis Testing (t-test, Mann-Whitney)ANOVA & Post-Hoc TestsCorrelation & Regression
R stats packageggplot2pheatmaplimma
⏱ 3 weeks · 30 hrs View Details →
🔍
MODULE 5
Sequence Analysis

BLAST, Multiple Sequence Alignment & Primer Design

Pairwise Sequence Alignment (Needleman-Wunsch, Smith-Waterman)BLAST: blastn, blastp, blastxMultiple Sequence Alignment (MSA)Scoring Matrices (BLOSUM, PAM)
BLAST+MUSCLEClustal OmegaPrimer3
⏱ 3 weeks · 30 hrs View Details →
🌐
MODULE 6
Introduction to Omics

Genomics, Transcriptomics, Proteomics & Metabolomics Overview

Genomics: Sequencing Technologies OverviewTranscriptomics: RNA-seq Workflow IntroductionProteomics: Mass Spectrometry BasicsMetabolomics: NMR & LC-MS Overview
Galaxy PlatformKEGG MapperReactomeGEO Database
⏱ 3 weeks · 30 hrs View Details →

🏆 Capstone Project

Choose one signature project to demonstrate your Level 1 mastery

🏆 RNA-seq DEG Analysis
🏆 Phylogenetic Tree Construction
🏆 Variant Annotation Pipeline
🏆 Simple Metabolomics Workflow

Earn Your Certificate

🎓

Bioinformatics Analyst

Awarded upon successful completion of all 6 modules and capstone project

🔬 LEVEL 2

Intermediate Bioinformatics

Develop analytical independence and full multi-omics capability.

6
Modules
220h
Total Hours
4
Capstone Options

6 Modules — Full Curriculum

Click any module to see full details, tools, practicals and learning outcomes

MODULE 1
Advanced Programming & Data Science

OOP, SciPy, Scikit-learn, Bioconductor & Shiny

Python OOP & Design PatternsNumPy & SciPy for Scientific ComputingScikit-learn: ML Basics for BioinformaticsBioconductor Ecosystem Overview
NumPySciPyScikit-learnBioconductor
⏱ 4 weeks · 40 hrs View Details →
🧬
MODULE 2
Next Generation Sequencing (NGS)

QC, Alignment, Variant Calling & GWAS

NGS Platform Technologies (Illumina, Nanopore)FASTQ Quality Control & TrimmingGenome Assembly StrategiesRead Mapping & Alignment
FastQCMultiQCTrimmomaticBWA
⏱ 4 weeks · 40 hrs View Details →
📈
MODULE 3
Transcriptomics

RNA-seq, Differential Expression & Functional Annotation

RNA-seq Experimental DesignHISAT2 & STAR AlignmentfeatureCounts / HTSeq QuantificationDESeq2 & edgeR Differential Expression
HISAT2STARfeatureCountsDESeq2
⏱ 4 weeks · 40 hrs View Details →
🕸️
MODULE 4
Functional Genomics

GO Analysis, Pathway Enrichment & Network Biology

Gene Ontology (GO) Terms & HierarchyPathway Databases: KEGG, Reactome, WikiPathwaysNetwork Biology FundamentalsProtein–Protein Interaction Networks
clusterProfilerGSEACytoscapeSTRING
⏱ 3 weeks · 30 hrs View Details →
⚗️
MODULE 5
Metabolomics & Proteomics

LC-MS/MS, Peak Detection, Annotation & Pathway Integration

Mass Spectrometry Principles (LC-MS/MS)Metabolomics Workflow: Extraction → Detection → AnalysisPeak Detection & Alignment (XCMS)Metabolite Annotation (CAMERA, HMDB)
XCMSCAMERAMetaboAnalystMaxQuant
⏱ 4 weeks · 40 hrs View Details →
🌳
MODULE 6
Comparative Genomics & Phylogenetics

Ortholog ID, Synteny, IQ-TREE & Evolutionary Analysis

Comparative Genomics ConceptsOrtholog & Paralog IdentificationSynteny AnalysisWhole Genome Alignment
OrthoFinderMAFFTIQ-TREEMEGA
⏱ 3 weeks · 30 hrs View Details →

🏆 Capstone Project

Choose one signature project to demonstrate your Level 2 mastery

🏆 Multi-Omics Integration Study
🏆 GWAS + Transcriptomics Pipeline
🏆 Metabolite-Gene Interaction Network
🏆 Comparative Genomics Study

Earn Your Certificate

🎓

Omics Data Scientist

Awarded upon successful completion of all 6 modules and capstone project

🚀 LEVEL 3

Advanced / Professional Bioinformatics

Train for industry, high-impact publications, and independent bioinformatics leadership.

8
Modules
290h
Total Hours
6
Capstone Options

8 Modules — Full Curriculum

Click any module to see full details, tools, practicals and learning outcomes

⚙️
MODULE 1
High-Performance Computing (HPC)

SLURM, Docker, Singularity, Nextflow & Cloud Pipelines

Linux Clusters & HPC ArchitectureJob Scheduling with SLURMParallel Computing & Multi-threadingContainer Technologies: Docker & Singularity
SLURMDockerSingularityNextflow
⏱ 3 weeks · 30 hrs View Details →
🤖
MODULE 2
AI & Machine Learning in Bioinformatics

Deep Learning, Feature Engineering & Gene Prediction

Supervised & Unsupervised Learning ReviewDeep Learning Architectures (CNN, RNN, Transformer)Transfer Learning for Biological SequencesFeature Engineering for Omics Data
TensorFlowPyTorchScikit-learnKeras
⏱ 4 weeks · 40 hrs View Details →
🔗
MODULE 3
Systems Biology & Multi-Omics Integration

Integrated Pipelines, Network Inference & Dynamic Modelling

Systems Biology PrinciplesMulti-Omics Data Integration StrategiesFactor Analysis Methods (MOFA, DIABLO)Gene Regulatory Network Inference
MOFA+DIABLO (mixOmics)GENIE3VIPER
⏱ 4 weeks · 40 hrs View Details →
🔵
MODULE 4
Single-Cell & Spatial Omics

scRNA-seq, Cell Trajectory, Spatial Transcriptomics

Single-Cell RNA-seq Technologies (10x Chromium, Drop-seq)Quality Control for scRNA-seqClustering & Cell Type AnnotationTrajectory / Pseudotime Analysis
SeuratScanpyMonocle3Harmony
⏱ 4 weeks · 40 hrs View Details →
🧩
MODULE 5
Structural Bioinformatics

Protein Structure, Molecular Docking & Dynamics

Protein Structure Hierarchy & Databases (PDB)Homology ModellingAlphaFold2 & ESMFold Structure PredictionMolecular Docking (AutoDock, HADDOCK)
AlphaFold2AutoDock VinaGROMACSPyMOL
⏱ 4 weeks · 40 hrs View Details →
🌾
MODULE 6
Advanced Genomics & Breeding Informatics

Pan-Genomics, CRISPR Informatics & Precision Breeding

Pan-Genome Concepts & Graph GenomesGenomic Selection & GS Models (GBLUP, rrBLUP)CRISPR-Cas9 Off-Target PredictionPopulation Genomics (Fst, LD, Selection Sweeps)
MinigraphrrBLUPCRISPORADMIXTURE
⏱ 4 weeks · 40 hrs View Details →
📝
MODULE 7
Scientific Communication & Reproducibility

Git, RMarkdown, Quarto, LaTeX & FAIR Data

Scientific Writing PrinciplesManuscript Structure & Journal FormattingPublication-Quality Figure PreparationFAIR Data Principles
GitGitHubQuartoR Markdown
⏱ 3 weeks · 30 hrs View Details →
🏭
MODULE 8
Industry & Translational Bioinformatics

Healthcare, Agriculture, Pharma & Biotech Applications

Clinical Genomics & Precision MedicinePharmacogenomics & Drug DiscoveryAgricultural Stress GenomicsGWAS in Breeding Pipelines
ClinVarPharmGKBDGIdbGalaxy
⏱ 3 weeks · 30 hrs View Details →

🏆 Capstone Project

Choose one signature project to demonstrate your Level 3 mastery

🏆 AI-Assisted Omics Prediction Model
🏆 Large-Scale GWAS Pipeline
🏆 Single-Cell Atlas Construction
🏆 Multi-Omics Stress Tolerance Framework
🏆 Protein Engineering Project
🏆 Population Genomics of Crop Adaptation

Earn Your Certificate

🎓

Computational Biologist

Awarded upon successful completion of all 8 modules and capstone project

🧬
Module 1 of 6

Biological Foundations

Central Dogma, Genetics & Genomic Databases

⏱ 3 weeks
📚 30 hrs
🎓 Level 1

📋 Core Topics Covered

Central Dogma of Molecular Biology
DNA / RNA / Protein structure
Gene Expression & Regulation
Chromosomes & Genome Organisation
Mutation, Variation & Polymorphism
Mendelian & Molecular Genetics
Cell Biology Essentials
Evolution & Phylogeny Basics

🔬 Lab Practicals & Exercises

▸ NCBI database exploration — Entrez, SRA, GEO
▸ Gene & protein sequence retrieval
▸ FASTA, GenBank, EMBL format handling
▸ Ensembl genome browser navigation
▸ UniProt protein annotation walkthrough

🎯 Learning Outcomes

By the end of this module, you will be able to:

Navigate all major biological databases confidently
Understand the molecular basis of heredity and gene expression
Read and interpret FASTA, GenBank, and GFF formats
Locate genes, transcripts, and protein records for any organism

🛠 Tools & Software

NCBI EntrezEnsembl BrowserUniProtExPASyPubMed
🧬

Ready to Start?

Join hundreds of researchers learning bioinformatics with KrishiGene

NEXT MODULE
Linux & Command Line →
🖥️
Module 2 of 6

Linux & Command Line

Bash, Shell Scripting & Remote Server Mastery

⏱ 3 weeks
📚 30 hrs
🎓 Level 1

📋 Core Topics Covered

Linux File System & Navigation
Bash Commands & Shortcuts
File Permissions & Ownership
Text Processing & Regex
Shell Scripting (loops, conditionals, functions)
SSH & Remote Server Setup
Environment Variables & PATH
Package Management (apt, conda)

🔬 Lab Practicals & Exercises

▸ FASTQ file manipulation & QC checks
▸ Directory organisation for bioinformatics projects
▸ Batch file processing scripts
▸ Writing reproducible bash pipelines
▸ Conda environment setup & management

🎯 Learning Outcomes

By the end of this module, you will be able to:

Navigate and manage Linux file systems fluently
Write shell scripts to automate repetitive bioinformatics tasks
Securely connect to and use remote HPC clusters
Process large text files (FASTQ, VCF, BED) from the command line

🛠 Tools & Software

grepawksedtmuxwgetcurlscreenconda
🖥️

Ready to Start?

Join hundreds of researchers learning bioinformatics with KrishiGene

NEXT MODULE
Programming for Bioinformatics →
🐍
Module 3 of 6

Programming for Bioinformatics

Python & R for Biological Data Science

⏱ 4 weeks
📚 40 hrs
🎓 Level 1

📋 Core Topics Covered

Python: Variables, Loops, Functions
Python: Pandas, NumPy, Biopython
Python: File I/O & Sequence Parsing
Python: Data Visualisation (Matplotlib, Seaborn)
R: Data frames & Tibbles
R: ggplot2 & dplyr
R: Statistical Analysis
R: Bioconductor Introduction

🔬 Lab Practicals & Exercises

▸ Sequence parsing scripts (FASTA, FASTQ, GenBank)
▸ Differential expression plots in R
▸ Automation scripts for file renaming, filtering
▸ Reading and writing bioinformatics file formats
▸ Building a BLAST result parser in Python

🎯 Learning Outcomes

By the end of this module, you will be able to:

Write production-quality Python scripts for sequence analysis
Perform data wrangling and visualisation in both Python and R
Parse common bioinformatics file formats programmatically
Build reusable bioinformatics utility functions

🛠 Tools & Software

Python 3BiopythonPandasR 4.xggplot2dplyrRStudioJupyter Notebook
🐍

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Statistics for Bioinformatics →
📊
Module 4 of 6

Statistics for Bioinformatics

Hypothesis Testing, PCA & Multiple Testing

⏱ 3 weeks
📚 30 hrs
🎓 Level 1

📋 Core Topics Covered

Probability Distributions
Hypothesis Testing (t-test, Mann-Whitney)
ANOVA & Post-Hoc Tests
Correlation & Regression
Multiple Testing Correction (Bonferroni, BH-FDR)
Principal Component Analysis (PCA)
Hierarchical Clustering
Statistical Power & Sample Size

🔬 Lab Practicals & Exercises

▸ Omics dataset statistical analysis in R
▸ Visualisation: heatmaps, volcano plots, PCA biplots
▸ Multiple testing correction on DEG results
▸ Correlation analysis across gene expression datasets

🎯 Learning Outcomes

By the end of this module, you will be able to:

Apply correct statistical tests to omics data
Interpret p-values, FDR, and effect sizes
Perform PCA and clustering for exploratory analysis
Communicate statistical results with publication-quality figures

🛠 Tools & Software

R stats packageggplot2pheatmaplimmaveganDESeq2 (intro)
📊

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Sequence Analysis →
🔍
Module 5 of 6

Sequence Analysis

BLAST, Multiple Sequence Alignment & Primer Design

⏱ 3 weeks
📚 30 hrs
🎓 Level 1

📋 Core Topics Covered

Pairwise Sequence Alignment (Needleman-Wunsch, Smith-Waterman)
BLAST: blastn, blastp, blastx
Multiple Sequence Alignment (MSA)
Scoring Matrices (BLOSUM, PAM)
Motif Finding & Scanning
Primer Design Principles
Restriction Enzyme Analysis
Sequence Logo & Conservation

🔬 Lab Practicals & Exercises

▸ BLAST searches on NCBI & local BLAST
▸ MUSCLE and Clustal Omega MSA runs
▸ Primer3 primer design for PCR
▸ Motif discovery using MEME suite
▸ Conservation analysis with JalView

🎯 Learning Outcomes

By the end of this module, you will be able to:

Run and interpret BLAST searches confidently
Build multiple sequence alignments for any protein/gene family
Design PCR primers with correct Tm and GC considerations
Identify conserved motifs across related sequences

🛠 Tools & Software

BLAST+MUSCLEClustal OmegaPrimer3MEME SuiteJalViewEMBOSS Needle/Water
🔍

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Introduction to Omics →
🌐
Module 6 of 6

Introduction to Omics

Genomics, Transcriptomics, Proteomics & Metabolomics Overview

⏱ 3 weeks
📚 30 hrs
🎓 Level 1

📋 Core Topics Covered

Genomics: Sequencing Technologies Overview
Transcriptomics: RNA-seq Workflow Introduction
Proteomics: Mass Spectrometry Basics
Metabolomics: NMR & LC-MS Overview
Pathway Analysis (KEGG, Reactome)
Multi-Omics Integration Concept
Data Types & Formats in Each Omics Layer
Biological Interpretation Strategies

🔬 Lab Practicals & Exercises

▸ RNA-seq workflow overview (mock dataset)
▸ Differential expression analysis basics
▸ KEGG pathway mapping
▸ Gene set enrichment walkthrough
▸ Omics data integration introduction

🎯 Learning Outcomes

By the end of this module, you will be able to:

Understand the purpose and output of each omics layer
Navigate RNA-seq workflows from raw reads to DEGs
Map differentially expressed genes to biological pathways
Explain how multi-omics data is integrated for systems-level insights

🛠 Tools & Software

Galaxy PlatformKEGG MapperReactomeGEO DatabaseSTRING DB
🌐

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Capstone Project →
Module 1 of 6

Advanced Programming & Data Science

OOP, SciPy, Scikit-learn, Bioconductor & Shiny

⏱ 4 weeks
📚 40 hrs
🎓 Level 2

📋 Core Topics Covered

Python OOP & Design Patterns
NumPy & SciPy for Scientific Computing
Scikit-learn: ML Basics for Bioinformatics
Bioconductor Ecosystem Overview
ComplexHeatmap & Advanced R Visualisation
Shiny App Development
Pipeline Scripting with Snakemake (intro)
Data Structures for Omics (SummarizedExperiment)

🔬 Lab Practicals & Exercises

▸ Pipeline development with OOP design
▸ Interactive Shiny dashboards for omics data
▸ ML model for gene expression classification
▸ Advanced heatmaps with clinical annotations

🎯 Learning Outcomes

By the end of this module, you will be able to:

Build modular, reusable Python pipelines using OOP
Apply ML models to classify and cluster omics datasets
Create publication-quality complex heatmaps in R
Develop Shiny apps for interactive bioinformatics exploration

🛠 Tools & Software

NumPySciPyScikit-learnBioconductorComplexHeatmapShinySnakemake (intro)

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NEXT MODULE
Next Generation Sequencing →
🧬
Module 2 of 6

Next Generation Sequencing (NGS)

QC, Alignment, Variant Calling & GWAS

⏱ 4 weeks
📚 40 hrs
🎓 Level 2

📋 Core Topics Covered

NGS Platform Technologies (Illumina, Nanopore)
FASTQ Quality Control & Trimming
Genome Assembly Strategies
Read Mapping & Alignment
Variant Calling (SNPs, Indels, SVs)
Population Genetics Statistics
GWAS Fundamentals & Manhattan Plots
Annotation of Variants (SnpEff, VEP)

🔬 Lab Practicals & Exercises

▸ FastQC / MultiQC quality reports
▸ Trimmomatic / fastp trimming runs
▸ BWA-MEM & Bowtie2 alignment to reference genome
▸ GATK HaplotypeCaller variant calling pipeline
▸ BCFtools filtering & SNP annotation
▸ GWAS loci visualisation

🎯 Learning Outcomes

By the end of this module, you will be able to:

Execute complete NGS QC-to-variant pipelines
Interpret alignment metrics and variant call quality
Perform basic GWAS and interpret Manhattan/QQ plots
Annotate variants for functional impact

🛠 Tools & Software

FastQCMultiQCTrimmomaticBWABowtie2GATKSAMtoolsBCFtoolsSnpEffPLINK
🧬

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NEXT MODULE
Transcriptomics →
📈
Module 3 of 6

Transcriptomics

RNA-seq, Differential Expression & Functional Annotation

⏱ 4 weeks
📚 40 hrs
🎓 Level 2

📋 Core Topics Covered

RNA-seq Experimental Design
HISAT2 & STAR Alignment
featureCounts / HTSeq Quantification
DESeq2 & edgeR Differential Expression
Isoform Analysis (rMATS, StringTie)
Volcano & MA Plot Interpretation
GO Enrichment Analysis
KEGG Pathway Visualisation

🔬 Lab Practicals & Exercises

▸ End-to-end RNA-seq: reads → counts → DEGs
▸ Volcano plots with ggplot2
▸ GO and KEGG enrichment with clusterProfiler
▸ Isoform switching analysis
▸ Comparative transcriptomics across treatments

🎯 Learning Outcomes

By the end of this module, you will be able to:

Design and execute complete RNA-seq analysis pipelines
Identify, validate, and annotate differentially expressed genes
Visualise results with publication-quality volcano and heatmap plots
Link DEGs to biological functions and disease pathways

🛠 Tools & Software

HISAT2STARfeatureCountsDESeq2edgeRclusterProfilerpathviewrMATS
📈

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NEXT MODULE
Functional Genomics →
🕸️
Module 4 of 6

Functional Genomics

GO Analysis, Pathway Enrichment & Network Biology

⏱ 3 weeks
📚 30 hrs
🎓 Level 2

📋 Core Topics Covered

Gene Ontology (GO) Terms & Hierarchy
Pathway Databases: KEGG, Reactome, WikiPathways
Network Biology Fundamentals
Protein–Protein Interaction Networks
Co-expression Network Analysis (WGCNA)
Regulatory Genomics (ChIP-seq, ATAC-seq intro)
TF Binding Motif Analysis

🔬 Lab Practicals & Exercises

▸ GO enrichment dot plots & bar charts
▸ Gene–metabolite interaction networks in Cytoscape
▸ Co-expression module detection with WGCNA
▸ STRING PPI network construction
▸ TF motif enrichment in DEG promoters

🎯 Learning Outcomes

By the end of this module, you will be able to:

Perform and visualise GO and pathway enrichment analyses
Build and interpret biological interaction networks
Identify hub genes in co-expression modules
Connect gene regulation to downstream metabolic effects

🛠 Tools & Software

clusterProfilerGSEACytoscapeSTRINGWGCNAHOMERMEME-ChIP
🕸️

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NEXT MODULE
Metabolomics & Proteomics →
⚗️
Module 5 of 6

Metabolomics & Proteomics

LC-MS/MS, Peak Detection, Annotation & Pathway Integration

⏱ 4 weeks
📚 40 hrs
🎓 Level 2

📋 Core Topics Covered

Mass Spectrometry Principles (LC-MS/MS)
Metabolomics Workflow: Extraction → Detection → Analysis
Peak Detection & Alignment (XCMS)
Metabolite Annotation (CAMERA, HMDB)
Proteomics: Database Search & Quantification
Peptide Identification (Mascot, MaxQuant)
Differential Abundance Analysis
Metabolic Pathway Integration

🔬 Lab Practicals & Exercises

▸ XCMS peak picking and alignment
▸ CAMERA annotation run
▸ MetaboAnalyst PCA & PLS-DA
▸ Volcano and pathway plots for metabolomics
▸ Label-free quantification proteomics walkthrough

🎯 Learning Outcomes

By the end of this module, you will be able to:

Process raw LC-MS data from peak detection to annotated metabolites
Apply multivariate statistics (PCA, PLS-DA) to metabolomics data
Integrate metabolomics and proteomics results with genomics
Build metabolic pathway maps from experimental data

🛠 Tools & Software

XCMSCAMERAMetaboAnalystMaxQuantPerseusHMDBMetaCyc
⚗️

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NEXT MODULE
Comparative Genomics & Phylogenetics →
🌳
Module 6 of 6

Comparative Genomics & Phylogenetics

Ortholog ID, Synteny, IQ-TREE & Evolutionary Analysis

⏱ 3 weeks
📚 30 hrs
🎓 Level 2

📋 Core Topics Covered

Comparative Genomics Concepts
Ortholog & Paralog Identification
Synteny Analysis
Whole Genome Alignment
Phylogenomics Pipelines
Maximum Likelihood & Bayesian Phylogenetics
Molecular Clock Analysis
Genome Rearrangements & Evolution

🔬 Lab Practicals & Exercises

▸ OrthoFinder ortholog clustering
▸ Synteny visualisation with MCScanX
▸ IQ-TREE phylogenomic analysis
▸ MEGA tree building and annotation
▸ ggtree visualisation in R
▸ Whole genome alignment with MUMmer

🎯 Learning Outcomes

By the end of this module, you will be able to:

Identify orthologs and paralogs across multiple genomes
Build and interpret maximum likelihood phylogenetic trees
Visualise synteny and genome rearrangements
Estimate divergence times using molecular clocks

🛠 Tools & Software

OrthoFinderMAFFTIQ-TREEMEGAggtreeMCScanXMUMmerBEAST2
🌳

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NEXT MODULE
Capstone Project →
⚙️
Module 1 of 8

High-Performance Computing (HPC)

SLURM, Docker, Singularity, Nextflow & Cloud Pipelines

⏱ 3 weeks
📚 30 hrs
🎓 Level 3

📋 Core Topics Covered

Linux Clusters & HPC Architecture
Job Scheduling with SLURM
Parallel Computing & Multi-threading
Container Technologies: Docker & Singularity
Workflow Management: Nextflow & Snakemake
Cloud Computing (AWS, Google Cloud basics)
Reproducible Research Environments
Pipeline Benchmarking & Optimisation

🔬 Lab Practicals & Exercises

▸ SLURM job submission scripts
▸ Containerised RNA-seq pipeline with Nextflow
▸ Snakemake DAG pipeline construction
▸ Docker image creation for bioinformatics tools
▸ Cloud-based genome analysis run

🎯 Learning Outcomes

By the end of this module, you will be able to:

Submit and manage jobs on HPC clusters using SLURM
Build reproducible containerised bioinformatics pipelines
Design scalable Nextflow/Snakemake workflows
Deploy and run pipelines on cloud infrastructure

🛠 Tools & Software

SLURMDockerSingularityNextflowSnakemakeAWS Batchnf-core pipelines
⚙️

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NEXT MODULE
AI & Machine Learning →
🤖
Module 2 of 8

AI & Machine Learning in Bioinformatics

Deep Learning, Feature Engineering & Gene Prediction

⏱ 4 weeks
📚 40 hrs
🎓 Level 3

📋 Core Topics Covered

Supervised & Unsupervised Learning Review
Deep Learning Architectures (CNN, RNN, Transformer)
Transfer Learning for Biological Sequences
Feature Engineering for Omics Data
Gene Prediction with ML
Protein Structure Prediction (AlphaFold concepts)
Biomarker Discovery with ML
Model Evaluation & Validation

🔬 Lab Practicals & Exercises

▸ CNN model for promoter sequence prediction
▸ Random forest for biomarker selection from RNA-seq
▸ LSTM model for gene expression prediction
▸ AlphaFold2 structure prediction run
▸ Model interpretation with SHAP values

🎯 Learning Outcomes

By the end of this module, you will be able to:

Build and train deep learning models on biological sequence data
Apply transfer learning to leverage pre-trained biological models
Discover biomarkers using ensemble ML methods
Evaluate model performance with biologically meaningful metrics

🛠 Tools & Software

TensorFlowPyTorchScikit-learnKerasSHAPESMFoldAlphaFold2 (API)
🤖

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NEXT MODULE
Systems Biology & Multi-Omics →
🔗
Module 3 of 8

Systems Biology & Multi-Omics Integration

Integrated Pipelines, Network Inference & Dynamic Modelling

⏱ 4 weeks
📚 40 hrs
🎓 Level 3

📋 Core Topics Covered

Systems Biology Principles
Multi-Omics Data Integration Strategies
Factor Analysis Methods (MOFA, DIABLO)
Gene Regulatory Network Inference
Flux Balance Analysis (FBA)
Dynamic Biological Modelling (ODE systems)
Network Perturbation Analysis
Phenotype–Genotype Mapping

🔬 Lab Practicals & Exercises

▸ MOFA multi-omics factor analysis
▸ Joint pathway enrichment across omics layers
▸ GRN inference with GENIE3
▸ FBA metabolic flux modelling
▸ Systems-level interpretation of stress response data

🎯 Learning Outcomes

By the end of this module, you will be able to:

Integrate transcriptome, proteome, and metabolome datasets
Infer gene regulatory networks from multi-omics data
Perform metabolic flux analysis
Identify key system-level drivers of biological phenotypes

🛠 Tools & Software

MOFA+DIABLO (mixOmics)GENIE3VIPERCOBRApyCellChatiGraph
🔗

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NEXT MODULE
Single-Cell & Spatial Omics →
🔵
Module 4 of 8

Single-Cell & Spatial Omics

scRNA-seq, Cell Trajectory, Spatial Transcriptomics

⏱ 4 weeks
📚 40 hrs
🎓 Level 3

📋 Core Topics Covered

Single-Cell RNA-seq Technologies (10x Chromium, Drop-seq)
Quality Control for scRNA-seq
Clustering & Cell Type Annotation
Trajectory / Pseudotime Analysis
Doublet Detection & Batch Correction
Spatial Transcriptomics (Visium, MERFISH)
Ligand–Receptor Interaction Analysis
Multi-Sample & Multi-Condition Analysis

🔬 Lab Practicals & Exercises

▸ Seurat end-to-end scRNA-seq pipeline
▸ Monocle3 trajectory analysis
▸ Scanpy Python-based clustering
▸ Spatial deconvolution with RCTD
▸ Cell–cell communication with CellChat
▸ Batch correction with Harmony / scVI

🎯 Learning Outcomes

By the end of this module, you will be able to:

Process 10x Chromium scRNA-seq data end-to-end
Annotate cell types using marker genes and reference atlases
Infer cell differentiation trajectories
Integrate spatial context with single-cell transcriptomics

🛠 Tools & Software

SeuratScanpyMonocle3HarmonyCellChatRCTDscVISquidpy
🔵

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NEXT MODULE
Structural Bioinformatics →
🧩
Module 5 of 8

Structural Bioinformatics

Protein Structure, Molecular Docking & Dynamics

⏱ 4 weeks
📚 40 hrs
🎓 Level 3

📋 Core Topics Covered

Protein Structure Hierarchy & Databases (PDB)
Homology Modelling
AlphaFold2 & ESMFold Structure Prediction
Molecular Docking (AutoDock, HADDOCK)
Molecular Dynamics Simulation Basics
Virtual Screening Pipelines
Protein–Ligand Interaction Analysis
Drug Discovery Informatics

🔬 Lab Practicals & Exercises

▸ AlphaFold2 structure prediction for plant proteins
▸ AutoDock Vina docking run
▸ GROMACS MD simulation setup and run
▸ PyMOL structure visualisation & figure generation
▸ Pharmacophore modelling for agrochemical leads

🎯 Learning Outcomes

By the end of this module, you will be able to:

Predict and evaluate 3D protein structures with AlphaFold2
Perform molecular docking to identify protein–ligand interactions
Set up and run molecular dynamics simulations
Apply structural insights to drug/agrochemical discovery

🛠 Tools & Software

AlphaFold2AutoDock VinaGROMACSPyMOLHADDOCKChimera UCSFOpen BabelRDKit
🧩

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NEXT MODULE
Advanced Genomics & Breeding →
🌾
Module 6 of 8

Advanced Genomics & Breeding Informatics

Pan-Genomics, CRISPR Informatics & Precision Breeding

⏱ 4 weeks
📚 40 hrs
🎓 Level 3

📋 Core Topics Covered

Pan-Genome Concepts & Graph Genomes
Genomic Selection & GS Models (GBLUP, rrBLUP)
CRISPR-Cas9 Off-Target Prediction
Population Genomics (Fst, LD, Selection Sweeps)
QTL Mapping & Fine Mapping
Genomic Prediction for Crop Improvement
Stress Tolerance Genomics
Breeding Value Estimation

🔬 Lab Practicals & Exercises

▸ Minigraph pangenome construction
▸ rrBLUP genomic selection model
▸ CRISPR guide RNA design with CRISPOR
▸ Population structure analysis with ADMIXTURE
▸ QTL mapping with R/qtl
▸ Selection sweep detection (XP-CLR, iHS)

🎯 Learning Outcomes

By the end of this module, you will be able to:

Build and navigate pan-genomic datasets for crops
Design and evaluate CRISPR guide RNAs in silico
Run genomic selection models for breeding applications
Identify selection sweeps and QTLs in crop populations

🛠 Tools & Software

MinigraphrrBLUPCRISPORADMIXTUREPLINK2R/qtlPopLDdecayHaploview
🌾

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NEXT MODULE
Scientific Communication →
📝
Module 7 of 8

Scientific Communication & Reproducibility

Git, RMarkdown, Quarto, LaTeX & FAIR Data

⏱ 3 weeks
📚 30 hrs
🎓 Level 3

📋 Core Topics Covered

Scientific Writing Principles
Manuscript Structure & Journal Formatting
Publication-Quality Figure Preparation
FAIR Data Principles
Git & GitHub for Science
R Markdown & Quarto Reports
LaTeX for Scientific Documents
Data Repository Submission (Zenodo, GEO, NCBI SRA)

🔬 Lab Practicals & Exercises

▸ GitHub repository setup for a bioinformatics project
▸ Quarto reproducible analysis report
▸ LaTeX manuscript template
▸ Figure preparation for Nature/Science submission
▸ Data submission to GEO / NCBI SRA

🎯 Learning Outcomes

By the end of this module, you will be able to:

Write clear, structured scientific manuscripts
Create publication-quality figures meeting journal standards
Manage code and data with version control (Git)
Deposit datasets to public repositories following FAIR principles

🛠 Tools & Software

GitGitHubQuartoR MarkdownLaTeX (Overleaf)ZenodoInkscapeAdobe Illustrator
📝

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NEXT MODULE
Industry & Translational Bioinformatics →
🏭
Module 8 of 8

Industry & Translational Bioinformatics

Healthcare, Agriculture, Pharma & Biotech Applications

⏱ 3 weeks
📚 30 hrs
🎓 Level 3

📋 Core Topics Covered

Clinical Genomics & Precision Medicine
Pharmacogenomics & Drug Discovery
Agricultural Stress Genomics
GWAS in Breeding Pipelines
Synthetic Biology Design Tools
Regulatory Bioinformatics (FDA, CLIA)
Bioinformatics Consulting & Project Management
Career Pathways in Industry

🔬 Lab Practicals & Exercises

▸ Clinical variant interpretation (ACMG guidelines)
▸ Drug–gene interaction analysis
▸ Crop stress genomics case study
▸ Synthetic biology part design with iGEM tools
▸ Mock bioinformatics project scoping exercise

🎯 Learning Outcomes

By the end of this module, you will be able to:

Translate bioinformatics skills to healthcare, pharma, and agri industries
Interpret clinical variant reports using ACMG guidelines
Navigate regulatory requirements for bioinformatics in clinical settings
Position yourself effectively for industry roles

🛠 Tools & Software

ClinVarPharmGKBDGIdbGalaxySynBioHubOpenSNPOMIMClinicalTrials.gov
🏭

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NEXT MODULE
Capstone Project →
💬