BIONFORMATICS PROJECTS
1. Database Development Projects
2. Analytical Projects
3. Software Development Projects
4. IN-SILICO Drug Discovery Projects
5. Development of Bioinformatics Education Materials Projects
1. Database Development Projects
Objective of the Project
This project will allow students to develop background knowledge as well as core expertise in Database Management Systems. The students will learn Database concept, Data Structure, Data Models, various approaches to Database design, strengths of relational model, Normalization.
At the end of the project the student will be able to
• Understand Database design and normalization techniques.
• Use Standard Query Language and its various versions.
• Understand Importance of backup and recovery techniques.
• Develop Database system to handle the real world problem
Software's Used:
1. JAVA 2. MSQL Server 2005/ Oracle
(OR)
2. ASP.NET 2. MSQL Server 2005/ Oracle
Sample Project titles
Automation of suitable diseases
Management of suitable proteins
Enzyme management system
Metabolic pathway management system
Genome mapping databases
Organism specific databases
2. ANALYTICAL Projects
Objective of the Project
The rapidly increasing number of nucleotide and amino acid sequence data has become a major source of information for biomedical researchers. We think that this Sequence Analysis project is an important part of the training of every student in biology or biochemistry.
* To ensure familiarity with basic computer concepts and their everyday use in a biological laboratory setting.
* To acquaint the students with the structure of molecular sequence databases and with the methods to analyze their contents.
* To present some of the biological resources available on the Internet and their usefulness (or lack thereof).
Sample Project titles
A) Comparative Genomics
1.COG 2. GENOME BLAST 3. MBGD 4. PEDANT 5. VISTA 6. BLAST2SEQ
B) Phylogenetic analysis
1.Phylip 2. Treetop 3. Phylodraw
C) Structure and function prediction
1. Primary Structure - PROPSEARCH, COMPUTE Pi/ MW
2. Secondary Structure - SOPMA, NN-PREDICT
3. Tertiary Structure - SWISS MODEL
4. Specialized Structure - COILS2, SIGNAL P
D) Multiple sequence alignment (MSA)
1. Repeat Masker 2. GCUA 3. EMBOSS TRANSEQ 4.CLUSTAL W 5. MAST 6. PFAM
7 ORF Finder
E) QSAR studies
1. Hyperchem
3. Software Development Projects
Bioprogramming and BioImaging
Objective of the Project
The first phase of project development is bioprogramming. This involves basic project planning and assembly of the design criteria, and includes quantification of all project components which describe functions and operations. Bioprogramming can be simple or detailed, depending on the nature and purpose of the project. Although frequently overlooked, bioprogramming is the most vital phase. Thorough effort at this time makes all subsequent stages easier, and avoids future complications and disagreements.
Software's Used:
PERL, JAVA, .NET, FLASH,FLEX
Sample Project titles
Nucleotide content prediction tool
Aminoacid content prediction tool
Protein Amplification Restriction tool
4. IN-SILICO Drug Discovery Projects
Objective of the Project
Learning Objectives after this project you should be able to: Explain the individual steps involved in calculating a protein homology model. Identify suitable templates for modelling. Outline the principles behind ab initio protein structure prediction. Describe the differences between homology modelling and ab initio structure prediction. Describe the major pitfalls in protein modelling.
Software’s Used:
1. SWISS MODEL 2. SWISS PDB Viewer 3. RASMOL 4. SAVS 5. CASTp
Sample Project titles
Molecular modeling of pfEMP1 related with malarial diseases
Molecular docking of pfEMP1 with hydroxyl choloroquine
Drug designing and development of hydroxyl choloroquine
5. Development of Bioinformatics Education Materials Projects
Objective of the Project
Development of teaching & elearning modules in Bioinformatics
Effort for virtual experimental screening of chemical libraries with important targets from major infectious diseases Diseases
Proteins,Genes,etc.,
Software's Used:
Flash, Photoshop
Sample Project titles
Visual representation of process on Drug docking
Demonstration on any analytical methods
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Trying for job in Bioscience? Here is the way by clicking...
My Project Web Page & Sequence Analysis Tool using PERL & CGI
Sequence Analysis Tools
Aminoacid Content Prediction Tool(ACP)
Predicts total no. of aminoacids in a given query sequence.
Nucleotide Content Prediction Tool(NCP)
Predicts total no. of nucleotides in a given query sequence.
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What is Bioinformatics?
It's method to predict the biological outcomes before anyone go for full fledged research. It's a method to compare the biological data. Ex: sequence analysis. It's a way to predict or solve the protein structure.
It's the only way for PERSONALIZED MEDICINE in this post genomic era. It's the method to do comparative genomics and predict the Human homolog genes in other species.
It's the method to annotate the newly sequenced genomes.
How the biological problems can be predicted ?
We are living in the world of Computers. By analyzing the existing biological data using Information Technology we can predict the biological outcomes.
What is the HOTTEST branch of Bioinformaics in this post genomic era ?
Personalized medicine is the most hottest and fastest growing field. Personalized medicine can be achieved through bioinformatics only.
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Job opportunities in Bioinformatics
When we think about Job or Research after a degree in Bioinformatics, most of the people choose to do Ph.d in US and Europe.
Most of the European Universities prefer the students who are really interested in doing research for 3 - 4 years. Most of the universities don't expect TOEFL to apply for Ph.d.
American universities chose based on GRE and TOEFL scores to do Phd for 5 years.
Finally companies prefer the students who are strong in software side.
Love! is it Real.
If you've ever been in love, you've probably at least considered classifying the feeling as an addiction. And guess what: You were right. As it turns out, scientists are discovering that the same chemical process that takes place with addiction takes place when we fall in love.
Love is a chemical state of mind that's part of our genes and influenced by our upbringing. We are wired for romance in part because we are supposed to be loving parents who care diligently for our helpless babies.
In this we'll find out what love really is and what happens in our bodies that makes us fall in love -- and ensures we stay there. We'll also look at what attracts us to someone in the first place. Is it their pheromones, or do they just fit the right "love template?"
What is Love?
Photo courtesy Morgue FileRomantic love both exhilarates and motivates us. It is also critical to the continuation of our species. Without the attachment of romantic love, we would live in an entirely different society that more closely resembled some (but not all) of those social circles in the animal world. The chemicals that race around in our brain when we're in love serve several purposes, and the primary goal is the continuation of our species. Those chemicals are what make us want to form families and have children. Once we have children, those chemicals change to encourage us to stay together to raise those children. So in a sense, love really is a chemical addiction that occurs to keep us reproducing.
Regardless of the country or culture, romantic love plays an important part. While cultural differences in how that love is displayed vary greatly, the fact that romantic love exists is undisputed.
But let's get down to the nitty gritty. What is it that makes us fall in love with someone in the first place?
What Makes us Fall in Love?
©2002 FOX BROADCASTINGOn "24," Jack Bauer is involved with the Secretary of Defense's daughter, Audrey. Could it be she reminds him of his mother?-->We all have a template for the ideal partner buried somewhere in our subconscious. It is this love map that decides which person in that crowded room catches our eye. But how is this template formed?
Appearance
Many researchers have speculated that we tend to go for members of the opposite sex who remind us of our parents. Some have even found that we tend to be attracted to those who remind us of ourselves. In fact, cognitive psychologist David Perrett, at the University of St. Andrews in Scotland, did an experiment in which he morphed a digitized photo of the subject's own face into a face of the opposite sex. Then, he had the subject select from a series of photos which one he or she found most attractive. According to Dr. Perrett, his subjects always preferred the morphed version of their own face (and they didn't recognize it as their own).
Personality
Like appearance, we tend to form preferences for those who remind us of our parents (or others close to us through childhood) because of their personality, sense of humor, likes and dislikes, etc.
Pheromones
The debated topic of human pheromones still carries some weight in the field of love research. The word "pheromone" comes from the Greek words pherein and hormone, meaning "excitement carrier".
In the animal world, pheromones are individual scent "prints" found in urine or sweat that dictate sexual behavior and attract the opposite sex. They help animals identify each other and choose a mate with an immune system different enough from their own to ensure healthy offspring. They have a special organ in their noses called the vomeronasal organ (VNO) that detects this odorless chemical.
The existence of human pheromones was discovered in 1986 by scientists at the Chemical Senses Center in Philadelphia and its counterpart in France. They found these chemicals in human sweat. A human VNO has also been found in some, but not all, people. Even if the VNO isn't present in all of us -- and may not be working in those who do have it -- there is still evidence that smell is an important aspect of love (note the booming perfume industry). An experiment was conducted where a group of females smelled the unwashed tee shirts of a group of sweaty males, and each had to select the one to whom she was most "attracted." Just like in the animal world, the majority of the females chose a shirt from the male whose immune system was the most different from their own.
Staring Into Each Other's Eyes
Professor Arthur Aron, of the State University of New York at Stonybrook, has studied what happens when people fall in love and has found that simply staring into each other's eyes has tremendous impact.
In an experiment he conducted, Professor Aron put strangers of the opposite sex together for 90 minutes and had them discuss intimate details about themselves. He then had them stare into each other's eyes for four minutes without talking. The results? Many of the subjects felt a deep attraction for their partner after the experiment, and two even ended up getting married six months later.
Aphrodisiacs
According to the Food and Drug Administration, aphrodisiacs are based in "folklore, not fact." Still, people continue to believe in the love-inducing effects of certain foods, herbs and extracts. There are several common aphrodisiacs that may or may not have actual effects on your love life. Discovery Health listed some of these:
Asparagus: The vitamin E in this vegetable is said to stimulate sex hormones.
Chili peppers: Some researchers say that eating hot peppers makes us release endorphins, which might lead to "other things."
Chocolate: This favorite for Valentine's Day contains phenylethylamine, one of the chemicals your body produces naturally when you're in love.
Oysters: Oysters contain high levels of zinc, which reportedly increased the production of testosterone. Testosterone increases libido for both sexes.
Others include Ginkgo, Spanish fly (dead beetle parts) and Damiana.
Most of these are supposed to create the desire for sex or improve male sexual ability rather than attract a mate. But, if you're stimulating hormones that make you more interested, then you're more likely to meet someone and fall in love. And, even if they don't actually work, some say that if you think it's going to work, you're halfway there.
Types/Stages of Love:
There are three distinct types or stages of "love":
Lust, or erotic passion
Attraction, or romantic passion
Attachment, or commitment
When all three of these happen with the same person, you have a very strong bond. Sometimes, however, the one we lust after isn't the one we're actually in love with.
Lust
When we're teenagers, just after puberty, estrogen and testosterone become active in our bodies for the first time and create the desire to experience "love." These desires, a.k.a. lust, play a big role both during puberty and throughout our lives. According to an article by Lisa Diamond, entitled "Love and Sexual Desire" (Current Directions in Psychological Science, vol 13 no. 3), lust and romantic love are two different things caused by different underlying substrates. Lust evolved for the purpose of sexual mating, while romantic love evolved because of the need for infant/child bonding. So even though we often experience lust for our romantic partner, sometimes we don't -- and that's okay. Or, maybe we do, but we also lust after someone else. According to Dr. Diamond, that's normal.
Sexologist John Money draws the line between love and lust in this way: "Love exists above the belt, lust below. Love is lyrical. Lust is lewd."
Pheromones, looks and our own learned predispositions for what we look for in a mate play an important role in whom we lust after, as well. Without lust, we might never find that special someone. But, while lust keeps us "looking around," it is our desire for romance that leads us to attraction.
Attraction
While the initial feelings may (or may not) come from lust, what happens next -- if the relationship is to progress -- is attraction. When attraction, or romantic passion, comes into play, we often lose our ability to think rationally -- at least when it comes to the object of our attraction. The old saying "love is blind" is really accurate in this stage. We are often oblivious to any flaws our partner might have. We idealize them and can't get them off our minds. This overwhelming preoccupation and drive is part of our biology. We'll go deeper into the chemicals involved in attraction in The Chemistry of Love.
In this stage, couples spend many hours getting to know each other. If this attraction remains strong and is felt by both of them, then they usually enter the third stage: attachment.
Attachment
Photo courtesy Morgue FileThe attachment, or commitment, stage is love for the duration. You've passed fantasy love and are entering into real love. This stage of love has to be strong enough to withstand many problems and distractions. Studies by University of Minnesota researcher Ellen Berscheid and others have shown that the more we idealize the one we love, the stronger the relationship during the attachment stage.
Psychologists at the University of Texas in Austin have come to the same conclusion. They found that idealization appears to keep people together and keep them happier in marriage. "Usually, this is a matter of one person putting a good spin on the partner, seeing the partner as more responsive than he or she really is," says Ted Huston, the study's lead investigator. "People who do that tend to stay in relationships longer than those who can't or don't."
Playing a key role in this stage are oxytocin, vasopressin and endorphins, which are released when having sex.
Let's find out more about the chemistry of love.
The Chemistry of Love
There are a lot of chemicals racing around your brain and body when you're in love. Researchers are gradually learning more and more about the roles they play both when we are falling in love and when we're in long-term relationships. Of course, estrogen and testosterone play a role in the sex drive area. Without them, we might never venture into the "real love" arena.
That initial giddiness that comes when we're first falling in love includes a racing heart, flushed skin and sweaty palms. Researchers say this is due to the dopamine, norepinephrine and phenylethylamine we're releasing. Dopamine is thought to be the "pleasure chemical," producing a feeling of bliss. Norepinephrine is similar to adrenaline and produces the racing heart and excitement. According to Helen Fisher, anthropologist and well-known love researcher from Rutgers University, together these two chemicals produce elation, intense energy, sleeplessness, craving, loss of appetite and focused attention. She also says, "The human body releases the cocktail of love rapture only when certain conditions are met and ... men more readily produce it than women, because of their more visual nature."
Researchers are using functional magnetic resonance imaging (fMRI) to watch people's brains when they look at a photograph of their object of affection. According to Helen Fisher, a well-known love researcher and an anthropologist at Rutgers University, what they see in those scans during that "crazed, can't-think-of-anything-but stage of romance" -- the attraction stage -- is the biological drive to focus on one person. The scans showed increased blood flow in areas of the brain with high concentrations of receptors for dopamine -- associated with states of euphoria, craving and addiction. High levels of dopamine are also associated with norepinephrine, which heightens attention, short-term memory, hyperactivity, sleeplessness and goal-oriented behavior. In other words, couples in this stage of love focus intently on the relationship and often on little else.
Another possible explanation for the intense focus and idealizing view that occurs in the attraction stage comes from researchers at University College London. They discovered that people in love have lower levels of serotonin and also that neural circuits associated with the way we assess others are suppressed. These lower serotonin levels are the same as those found in people with obsessive-compulsive disorders, possibly explaining why those in love "obsess" about their partner.
Chemical Bonding
Love JunkiesThere are those who may be addicted to that love "high." They need that amphetamine-like rush of dopamine, norepinephrine and phenylethylamine. Because the body builds up a tolerance to these chemicals, it begins to take more and more to give love junkies that high. They go through relationship after relationship to get their fix. In romantic love, when two people have sex, oxytocin is released, which helps bond the relationship. According to researchers at the University of California, San Francisco, the hormone oxytocin has been shown to be "associated with the ability to maintain healthy interpersonal relationships and healthy psychological boundaries with other people." When it is released during orgasm, it begins creating an emotional bond -- the more sex, the greater the bond. Oxytocin is also associated with mother/infant bonding, uterine contractions during labor in childbirth and the "let down" reflex necessary for breastfeeding.
Vasopressin, an antidiuretic hormone, is another chemical that has been associated with the formation of long-term, monogamous relationships. Dr. Fisher believes that oxytocin and vasopressin interfere with the dopamine and norepinephrine pathways, which might explain why passionate love fades as attachment grows.
Endorphins, the body's natural painkillers, also play a key role in long-term relationships. They produce a general sense of well-being, including feeling soothed, peaceful and secure. Like dopamine and norepinephrine, endorphins are released during sex; they are also released during physical contact, exercise and other activities. According to Michel Odent of London's Primal Health Research Center, endorphins induce a "drug-like dependency."
The Long Haul?
What about when that euphoric feeling is gone? According to Ted Huston at the University of Texas, the speed at which courtship progresses often determines the ultimate success of the relationship. What they found was that the longer the courtship, the stronger the long-term relationship.
The feelings of passionate love, however, do lose their strength over time. Studies have shown that passionate love fades quickly and is nearly gone after two or three years. The chemicals responsible for "that lovin' feeling" (adrenaline, dopamine, norepinephrine, phenylethylamine, etc.) dwindle. Suddenly your lover has faults. Why has he or she changed, you may wonder. Actually, your partner probably hasn't changed at all; it's just that you're now able to see him or her rationally, rather than through the blinding hormones of infatuation and passionate love. At this stage, the relationship is either strong enough to endure, or the relationship ends.
If the relationship can advance, then other chemicals kick in. Endorphins, for example, are still providing a sense of well-being and security. Additionally, oxytocin is still released when you're having sex, producing feelings of satisfaction and attachment. Vasopressin also continues to play a role in attachment.
Are We Alone in Love?
The prairie vole is one such animal. This vole mates for life and prefers spending time with its mate over spending time with any other voles. Voles even go to the extreme of avoiding voles of the opposite sex.
When they have offspring, the couple works together to care for them. They spend hours grooming each other and just hanging out together. Studies have been done to try to determine the chemical makeup that might explain why the prairie vole forms this lifelong, monogamous relationship when its very close relative, the montane vole, does not.
According to studies by Larry Young, a social attachment researcher at Emory University, what happens is that when the prairie vole mates, like humans, the hormones oxytocin and vasopressin are released. Because the prairie vole has the needed receptors in its brain for these hormones in the regions responsible for reward and reinforcement, it forms a bond with its mate. That bond is for that particular vole based on its smell -- sort of like an imprint. As further reinforcement, dopamine is also released in the brain's reward center when they have sex, making the experience enjoyable and ensuring that they want to do it again. And because of the oxytocin and vasopressin, they want to have sex with the same vole.
Because the montane vole does not have receptors for oxytocin or vasopressin in its brain, those chemicals have no effect, and they continue with their one-night stands. Other than those receptors, the two vole species are almost entirely the same in their physical makeup.
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