Virtual Labs from Amrita Vishwa Vidyapeeth for Biotechnology and Biomedical Engineering

Biotechnology and Biomedical Engineering

Biosignal Processing and Analysis
This lab focuses on using, analysing and processing EEG data and provides a platform for EEG data analysis and visualization, to understand the correlations of neural activity through electroencephalography data. The lab is an education platform for engineers and biologists without major requirements for learning methods in signal processing.


Bioinformatics and Data Science in Biotechnology
This lab is a connection of bioinformatics experiments performed using R programming. Educating this will allow users to learn how to use R as an open source language for learning bioinformatics data processing. Specifically, this lab will help analyse biological sequence data using simple R code snippets.

Writing and Reading Sequence Data in R || Pairwise sequence alignment of Protein or DNA sequences || Guanine-Cytosine Content Analysis and Basics of DNA Sequence Statistics
Neurophysiology Virtual Lab (pilot)
Neurophysiology is the study of nervous system function. Primarily, it is connected with neurobiology, psychology, neurology, clinical neurophysiology, electrophysiology, biophysical neurophysiology, ethology, neuroanatomy, cognitive science and other brain sciences.

Brain Slice Preparation || Simple Neuron Model - the HH neuron || Patch Clamp Technique || Current Clamp Technique || Voltage Clamp Technique || Study of Synaptic Transmission (Remote trigger) || Measuring Field Potentials Using MEA chips || Understanding the Passive Properties of a Simple Neuron (Remote trigger) || Effects of Ion Channels in Membrane Biophysics (Remote trigger) || Effect of Noise on Spiking Neurons (Remote trigger)
Neuron Simulation Virtual Lab (pilot)
This lab uses a graphical web-based Neuron simulator and models a section of excitable neuronal membrane using the Hodgkin-Huxley equations. Various experiments will deal with the several parameters of Hodgkin-Huxley equations and will model resting and action potentials, voltage and current clamp, pharmacological effects of drugs that block specific channels etc. This lab complements some of the exercises in the Virtual Neurophysiology lab.

Modeling resting potentials in Neurons || Modeling action potentials || Modeling the delayed rectifier Potassium channels || Modeling the sodium ion channel and its effects on neural signaling || Current Clamp protocol || Voltage Clamp Protocol || Understanding Frequency-Current relationship || Understanding first spike latency - current relationship || Voltage-Current (VI) plot || Effects of pharmacological blockers on action potential
Biochemistry Virtual Lab I
Biochemistry is the study of the chemical processes in living organisms. It deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules. The experiments included in Biochemistry Virtual Lab I are fundamental in nature, dealing with the identification and classification of various carbohydrates, acid-base titrations of amino acids, isolation of proteins from their natural sources, etc.

Qualitative Analysis of Carbohydrates || Isoelectric Precipitation of Proteins: Casein from Milk || Quantitative Estimation of Amino Acids by Ninhydrin || Separation of Amino Acids by Thin Layer Chromatography || Estimation of Saponification Value of Fats/Oils. || Detection of Adulteration in Milk || Qualitative Analysis of Amino Acid || Estimation of Iodine Value of Fats and Oils || Titration Curves of Aminoacids || Estimation of blood glucose by Glucose oxidase method
Biochemistry Virtual Lab II
Biochemistry Virtual Lab II deals with topics like enzymology, purification of plant pigments and natural products as well as estimation of iodine value and saponification value of fats and oils.

Isolation of β -Amylase from Sweet Potato || Gelatin Zymography || Extraction of Caffeine from Tea || Construction of Maltose Standard Curve by DNS Method || Isolation of Plant Pigments by Column Chromatography || Structural Studies of Phycobiliproteins from Spirulina || Construction of Protein Standard Curve using Folin’s Lowry Method || Effect of Substrate Concentration on Enzyme Kinetics || Effect of temperature on enzyme kinetics || Hydrolysis of Ester using orange peel esterase
Population ecology Virtual Lab I
A population is a collection of individuals of the same species that live together in a region. Population ecology is the study of populations (especially population abundance) and how they change over time. Crucial to this study are the various interactions between a population and its resources. Studies on simple models of interacting species is the main focus this simulation oriented lab. Lab I focuses on introduction of principles of population ecology for UG/PG students.

Population with Continuous and Discrete Growth || Spread of a Pest Population - Population Invasion || Age Structured Leslie Matrix || Stage Structured Leslie Matrix || Metapopulation Dynamics -Levins Model || Interspecific Competition and Coexistence || Effect of Interspecific Competition on Species Border || Logistic Population Growth: Continuous and Discrete || Parasitoid-Host Dynamics || Conserving an Endangered Species
Population ecology Virtual Lab II
Population ecology is the study of populations (especially population abundance) and how they change over time. Studies based on models of predation, competition as seen in interacting species is the main focus this simulation oriented lab. Lab II focuses on applied principles of population ecology for PG students.

Predator - Prey Dynamics - Rats and Snakes (Lotka Volterra Simulation) || Effect of Predator Efficiency on Equilibrium Densities & Pop. Stability || Effect of Social Behavior Amongst Predator-Prey Populations || Effects of Carrying Capacity and Satiation in Predator-Prey Dynamics || Harvesting a Prey Population || Optimal Foraging with Minimal Time: A Case of Searching Predators || Optimal Foraging : Searching Predators that Maximize Energy || Optimal Pollinators || Optimal Foraging: Sit-and-wait Predators that Maximize Energy || Microparasite and Macroparasite - Host Dynamics
Immunology Virtual Lab I
The branch of biomedicine concerned with the structure and function of the immune system, innate and acquired immunity, the bodily distinction of self from no self, and laboratory techniques involving the interaction of antigens with specific antibodies.

Collection of Serum from Blood || Blood Grouping Experiment || Latex Agglutination || INDIRECT Elisa || DIRECT Elisa || SANDWICH Elisa || ELISPOT Assay || Antibody Labeling with HRP || Extraction of IgG Antibodies from Immunized Hen Egg || Isolation of lymphocytes from whole blood
Immunology Virtual Lab II
The branch of biomedicine concerned with the structure and function of the immune system, innate and acquired immunity, the bodily distinction of self from no self, and laboratory techniques involving the interaction of antigens with specific antibodies.

Ouchterlony Double Diffusion -Titration || Ouchterlony Double Diffusion - Patterns || Purification of IgG Antibodies with Ammonium Sulphate || Removal of Thymus and Spleen from Mice || Mouse Anesthesia and Blood Collection || Parenteral Injections || Purification of IgG Antibodies using Affinity Chromatography || Fluorescent Labeling of Antibodies || Fragmentation of IgG Using Papain || Fragmentation of IgG using pepsin
Microbiology Virtual Lab I
The study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes such as fungi and, protists and prokaryotes. Viruses, though not strictly classed as living organisms, are also studied.

Gram Stain Technique || Aseptic Technique and the Transfer of Microorganisms || Streak Plate Method || Motility Test || Catalase and Coagulase Test || Lecithinase Test || Bacterial Growth Curve || Carbohydrate Fermentation Test || Differential and Cytological Staining Techniques || Antibiotic Susceptibility Testing || Methylene Blue Reductase Test
Microbiology Virtual Lab II
To study the biochemical properties of microorganisms, the various techniques employed in cultivation of fungi and viruses along with the molecular level analysis of microbial genome.

Voges-Proskauer Test || Triple Sugar Iron Agar || Urease Test || Litmus Milk Test || Slide Culture Technique for Fungi || Bacteriophage Plaque Assay for Phage Titer || Isolation and Identification of Auxotrophic and Drug Resistant Mutants || Isolation and Identification of Two Bacterial Unknowns || Routes of Viral Inoculation in Embryonated Eggs || 16S Ribosomal RNA Sequencing
Molecular Biology Virtual Lab I
The study of biology at a molecular level. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

Preparation of Buffer stocks (TBE,TE and TAE) || Plasmid Isolation (Mini prep) || Extraction of DNA from Fish Fins || Hot Shot Method of DNA Extraction || Agarose Gel Electrophoresis (AGE) || Restriction Digestion || Maintenance and Storage of DH5alpha E.coli cells || Preparation of Competent Cell (Calcium Chloride Treatment) || Transformation of the Host Cells || Extraction of DNA from Agarose gel
Molecular Biology Virtual Lab II
The study of biology at a molecular level. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

Preparation of Equilibrated Phenol || Isolation of RNA || Polyacrylamide Gel Electrophoresis || Ligation ( Using T4 DNA Ligase) || Polymerase Chain Reaction (PCR) || Electroblotting || Plating of the Bacteriophage || Plasmid Curing || Extraction of Bacteriophage DNA from Large Scale Cultures Using Proteinase K and SDS || Preparation of stocks of bacteriophage lambda by plate lysis and elution
Cell biology Virtual Lab I
Cell biology is an exciting and dynamic area that helps discover the fascinating world of cells. It includes the study of the structure and organization, growth, regulation, movements and interaction of the cells. Cell biology is closely related to other areas of biology such as genetics, molecular biology, and biochemistry.

Light Microscope || Cell Organization and Sub Cellular Structure Studies (Prokaryotic and Eukaryotic) || Transmission Electron Microscopy || Isolation of Mitochondria || Isolation of Chloroplast || Isolation of Endoplasmic Reticulum || Basics of Plant Tissue Culture || Glucose Uptake Assay || Transfection || Western Blotting
Cell biology Virtual Lab II
Cell biology is an exciting and dynamic area that helps discover the fascinating world of cells. It includes the study of the structure and organization, growth, regulation, movements and interaction of the cells. Cell biology is closely related to other areas of biology such as genetics, molecular biology, and biochemistry.

Lignin Staining || Hemocytometer (Counting of Cells) || Maintenance of Mamallian Cell Lines || Cell Attachment || Cell Migration || Actin Assembly || Mitosis in Onion Root Tips || Cell Proliferation || Toxicity studies in Zebrafish || Primary Cell Culture
Biological Image Analysis Virtual Lab
In this lab, UG/PG students will learn to use image processing techniques to analyze and quantify image data from wet lab experiments such as those in cell biology, biochemistry, molecular biology and immunology laboratories.

Introduction to Biological Image Analysis || Quantification of Lignin in Tissue Sections || Analysis of Cell Morphology || Counting of Fluorescent Particles || Counting of Total Fluorescence in a Cell || Analysis on Molecular Gels: A Case Study in Polyacrylamide Gel Electrophoresis || Quantification of Stained Liver Cells || Quantification of Bacterial Colonies on an Agar Plate || Quantification of Amino Acids Present in a Mixture || Quantification of Protein Present in a Sample
Bioinformatics Virtual Lab I
Bioinformatics is a field which using techniques of informatics to gather, store, analyse and integrate biological data. This virtual lab is an introductory course for undergraduate students and deals with the storage and retrieval of data from different biological databases like Gene, Pubmed, GEO, TAIR, Prosite etc.

Retrieving sequence data from Entrez || Locating the chromosome of a Gene || Retrieve gene expression data from GEO || Retrieving articles using PubMed || Finding ORF of a Given Sequence || Retrieving structural data of a protein using PDB database || Retrieving Motif Information of a Protein Using Prosite || Retrieving Gene Information from TAIR database || Designing a primer
Bioinformatics Virtual Lab II
This virtual laboratory is for undergraduate and postgraduate students to get a deeper understanding on the analysis of sequence data, its alignment and the evolutionary relationship. The exercises mainly deal with the different algorithms in sequence alignment and provides a computational exploration to the use of various tools used for sequence alignment.

Global alignment of two sequences - Needleman-Wunsch Algorithm || Smith-Waterman Algorithm - Local Alignment of Sequences || Pairwise Sequence Alignment using BLAST || Pairwise sequence alignment using FASTA || Aligning Multiple Sequences with CLUSTAL W || Construction of Cladogram || Phylogenetic Analysis using PHYLIP - Rooted trees || Phylogenetic Analysis using PHYLIP - Unrooted trees || Genome Annotation and Multiple Sequence Allignment.
Bioinformatics Virtual Lab III
In this virtual lab, one will study the computational analysis of proteins. This lab is targeted towards PG students with exercises that will allow one to learn visualising proteins in 3D, how to calculate distance among atoms, find active sites in protein structures and also delve into some structural analysis methods including docking and homology modeling. Combining labs 1, 2 and 3 will give an overall understanding of commonly used computational methods in bioinformatics.

Visualizing the Secondary Structure of a Protein || Calculating the Distance between the Ligand and a Particular Amino acid || Finding the Active Site Pockets of a given Protein Molecule || Primary Structure Analysis of a Protein Using ProtParam || Secondary structure analysis of a protein using SOPMA || Surface Analysis of a Protein Using CASTp || Retrieving details of a drug molecule || Converting chemical file formats || Homology Modeling using Modeller || Protein- Ligand Interaction
Systems Biology Virtual Lab
This virtual lab consist of modelling and simulation experiments for UG/PG students in bioinformatics and computational biology to understand biological processes using a systems biology approach.

Mathematical modeling and simulating of Biochemical network || Import and simulate models from different databases || To Import and simulate a model from the repository || SBML-A markup language for mathematical models in systems biology using cell designer || Creating and Visualizing a Simple Network Model || Analysis of biological networks for feature detection || Integrating Biological Networks and Microarray Expression data || Analyzing the network by finding sub modules
Computer-Aided Drug Design Virtual Lab
This lab is for PG students on the various laboratory topics in computer-aided drug design.

Constructing computational model of a molecule || Introducing Hydrogen atoms to a molecule || Dihedral angle calculation of a molecule || Energy minimization of a molecule || Predict the structure of protein-Homology Modeling || Drug-Receptor Interaction || Absorption and Distribution Property Prediction in Drug Designing Process || Toxicity prediction of a Molecule
Ecology Virtual Lab
Ecosystems are a complex and delicate balancing game.Ecosystems have an extremely complex web of cause and effect. The addition or removal of one species affects many other species with which it might compete for,or provide food.

Determination of pH of Waste Water Sample || Biological Oxygen Demand || Chemical Oxygen Demand of Waste water || Nitrogen Cycle || A Brief Introduction to Species Interactions in Ecology || Bacterial Population Growth || Population Invasion - A Threat to Ecosystem || Study of Foraging of Organisms in the Ecosystem || Case Studies on Ecology
Bio-inspired Robotics Virtual Labs (Remote Trigger)
This remote-triggerable online laboratory will teach experiments and offer to introduce biorobotics and neuronal robot techniques. The focus is on practical skills in using simple electronics to reinforce application of bio-inspired ideas. Many experiments will help working towards thesis projects.

Controlling a servo motor in a bio-robotic environment (Remote Trigger) || Understanding the kinematics of a robotic upper arm (Remote Trigger) || Understanding the kinematics of a robotic upper arm - Interactive (Remote Trigger) || Light sensing process in a neural circuit (Remote Trigger) || Pattern recognition in a hardware neural network (Remote Trigger) || Mechanism behind the movement of a Walker robot with 4 neurons (Remote Trigger) || Interaction study with Neuronal Circuits || Constructing a six core brain like circuit (Remote Trigger)
Virtual Biophysics Lab (Remote Trigger)
This lab will provide an online experience via remote equipment to study biophysics and biophysical techniques.

Using a light microscope (Remote Trigger) || Observing an animal cell using a light microscope (Remote Trigger) || Study of RC Properties of Cell Membrane (Remote Trigger) || Study of Electrically excitable cells (Remote trigger) || Bursting phenomenon in biology via RC models (Remote Trigger) || Micrometry (Remote Trigger) || Multicompartmental modelling of biophysical behaviour of neurons (Remote Trigger) || Understanding Photosynthesis as a Biologically Closed Process