Bioinformatics Software

DIAG has a variety of bioinformatics analysis tools pre-installed for the convenience of the user community. At this time, each access method has a different complement of software available for use. As the infrastructure continues to mature, we will deploy these applications such that they are available to all access methods. In addition, we will strive to maintain multiple versions of the most popular tools for those projects and users that need them.

Software

Name Version Shell/SSH Ergatis
454 X
abyss 1.3.4 X
allpathslg-42179 X
AmpliconNoise 1.25 X
augustus 2.5.5 X
BatMis 3 X X
bedtools 2.17.0 X
ber 20051118 X
BioPerl 1.6.1 X
blast 2.2.26 X
blat 35 X
bowtie2 2.0.0-beta7 X
bwa 0.6.2 X
cufflinks 2.0.2 X X
cummeRbund 2.0.0 X
dsrc 1.02 X
ELPH 1.0.1 X
EMBOSS 6.5.7 X X
exonerate 2.2.0 X
expat 2.1.0 X
fastx_toolkit 0.0.13 X
fastx_toolkit 0.0.13 X X
fcp 1.0.3 X
fr-hit v0.7-x86_64 X
FragGeneScan 1.16 X X
GeneMarkHMM 2.3d X
glimmer 3.0.2 X
gmap-gsnap 39648 X
gsl 1.9 X
hmmer 3.0 X X
ima 2-8.26.11 X
infernal 1.0.2 X
JAGS 3.2.0 X
jbrowse 1.2.1 X
jellyfish 1.1.4 X X
khmer X
kSNP v2 X
LipoP 1.0a X
mafft 7.029 X
maker 2.15 X
MEGAN 4.7 X
MetaGeneMark X
metAMOS 1.0b-june X
metaphlan 1.7.2 X
MetaVelvet 1.2.02 X
mothur 1.28.0 X
mpich2 1.4.1p1 X
mummer 3.2.3 X
NCBI-Blast 2.2.25+ X
PASA r2012-06-25 X
praze X
prodigal 2.6.0 X
Qiime 1.6.0 X
R 2.15.2 X X
RepeatMasker 3.3.0 X
rmblast 1.2 X
RNAmmer 1.2 X
samtools 0.1.18 X
samtools 0.1.18 X X
scons 2.2.0 X
signalp 4 X
snap 2010-07-28 X
SOAPdenovo 1.05 X
TMHMM 2.0c X
tophat 1.4.0 X X
trf 4.04 X
trinityrnaseq r2012-02-25 X
tRNAscan-SE 1.3.1 X
usearch 6.0.307 X
velvet 1.2.03 X
workflow 3.1.5 X X
WU-Blast 2.2.6 X

Improving Your Marketing Strategy Using Your Website

It is without any doubt that marketing is changing and what worked a while back may not necessarily produce the same results now. So as marketing continues to evolve so should your strategies and marketing efforts. There is always room for improvement and implementing new things may be exactly what you need to revolutionize your marketing efforts.

Focus on your target marketAlso, remember that there are very many marketing strategies out there and that does not mean you need to implement them all. No, on the contrary, the best way to ensure results is to analyze your target market and see which marketing channels and platforms will be best to get your sales up and running with the right demographic.

To effectively market your product or service, you need to know who your target market is, what their problems are, how your product or service is going to help them and finally where to find them. This is going to provide a clearer picture of what you need to achieve and how you are going to achieve it.

Six ways to improve your marketing strategy

  1. Make navigation easy

It is important that your site is easy to navigate. Make your customers or visitors experience a pleasant and worthwhile experience. Make it easy for them to find whatever content, product or service they are looking for. This is to avoid frustrating your customers which will leave them no choice but to click off your website.

The fewer the clicks, the more likely a sale will happen. Keep your customers in mind and position your navigation and landing tab in a way that is easy for them to see and find the categories they are most interested in.

  1. Optimize with keywords

Keywords are very useful because most of the people that visit your site will specifically be searching for certain terms that will lead them to you. These are the keywords that you need to focus more on. But how do you know which keywords they are? Well, by doing your research you will get to see what keywords perform best and apply them. Check out Google Adwords keywords and see the suggestions that pop up. In all this, be sure to keep the user’s intent in mind.

Using NYC search engine optimization services may also be able to optimize your site better and make it rank higher in the google searches. Using the right keywords and optimizing for the search engine will boost sales and improve your marketing efforts significantly.

  1. Include clear and precise calls to action

Have very clear calls to action on each page to ensure your visitors see them. These could either be connecting with your audience on social media, signing up for your newsletter or buying a product. The key thing here is being clear and telling your audience what you want them to do. This gives them the next step to take after visiting your site which may lead to conversions or new email subscribers.

Allow yourself to experiment with the placement of the call to action and see how they perform. It has been proven that the simplest of tweaks on your call to action may lead to an incredible increase in your CTR.

  1. Engage your visitors with visuals

When it comes to content marketing through your blog, it is important to use images that describe exactly what your blog post is about. Use videos, photos, and infographics for your benefit.

This will provide a good break from all the text and provide something appealing to the eye for your readers which will make them hang around longer. It is possible that a buying decision may be made by simply looking at a picture or watching the product in action.

Use banners that are visually appealing to capture the eye of your prospective client. This will draw them in to find out more from your site and see what it is all about.

  1. Valuable content

It is simply annoying when a business decides to the only blog about the feature of their products and why you should buy them. There are other ways to include your products in blog posts that actually give actionable information to your readers.

The best thing to do is to find a problem that your audience is facing and provide a solution to the problem. You could even include your product in there as a solution. This has a much better chance of working and persuading the readers to buy the product to ensure their problem is solved.

You should also remember to post consistently because people want reliable sources of information. To ensure you keep the engagement and subscribers coming you have to make time to write great content each week and post at the same times each week.

  1. Boost your website’s speed

Website speed mattersThe load time of your website should be as low as possible to avoid any time wastage. If your site happens to load too slow then you lose your prospects to your competitors. Not only that website speed is now used as a ranking signal by Google. This basically means that if your site’s load time is low, then you rank higher.

There are many ways you can boost your load time just start by testing it and continue on to fix the underlying problems that may be causing it. A faster loading site means a satisfied and frequent site visitor or even client.

Your website can serve you well and ensure your marketing strategy is delivering results. By simply optimizing your site to serve the needs of your clients and prospects, you get a huge increase in sales, engagement and even page views.

Take your time and test what works for you. Don’t be in a rush to implement anything just trust the process and be willing and open to learn and implement new things.

The best thing about using your site to market is that you can easily tweak what is not working and replace it with what is working. It is also a good idea to keep an eye on your competitors and see what strategies they are implementing and the return on investment.

Eye Color is the Result of Genetics, Pigmentation, and Melanin

The legendary actress Elizabeth Taylor has lovely, if rather unusual, lavender-colored eyes, while the late-and-great Paul Newman was noted for his “baby blues,” as was the pop icon Frank Sinatra. The distinguished actor Morgan Freeman, on the other hand, has big, dark liquid brown eyes that look almost black in certain lighting. So, what is it exactly that determines the color of someone’s eyes? Then again, to understand eye coloring, one must possess at least some basic knowledge of genetics and of the eye itself.

The Structure of the Eye

Approximately spherical, the eye is a sense organ that enables you to perceive light. It is basically similar to a camera, with the cornea and crystalline lens being comparable to the camera’s lens system, and the retina being comparable to the negative upon which an image is captured and photographed. Moreover, there are three main parts to the eye: the cornea, the retina, and the iris, although only the iris plays a role in determining eye color.

DNA involved in determining human eye colorThe Role and Function of the Iris

The iris is the colored part of the eye, in which is located the pupil (dark spot in the center of the eye). The iris contains two sets of muscles that dilate or constrict in order to acclimate the pupil to varying amounts of light. By constricting in bright light and dilating in low light, the iris increases one’s ability to see under even the most extreme conditions, for example, during a sudden power outage or when power is abruptly restored, although it usually takes the pupil a few minutes to adjust completely.

How Heredity Contributes to Eye Color

The amount of pigmentation in the eye and the pattern of that pigmentation are both determined by a person’s genetic makeup (DNA), which is provided by his or her parents. Some facts about genetics:

  • A human has 46 chromosomes divided into 23 pairs, with one chromosome in each pair inherited from the mother and one from the father.
  • The pieces of DNA on each chromosome are called genes, which are the basic units of heredity and determine physical characteristics.
  • The alleles within the genes determine the actual appearance of physical characteristics, for example, a person’s hair color, height, nose shape, and eye color.
  • For each inherited trait, there are two dominant alleles and two recessive genes.

Regarding how allele affects eye color, since green allele is dominant over blue, and the brown allele is dominant over both green and blue, the following results can be expected:

  • If a baby possesses a brown allele, he or she will have brown eyes.
  • If a baby has a green allele on chromosome 19, but all others are blue, he or she will have green eyes.
  • If all four alleles are blue, a baby will have blue eyes since only two blue-eye genes produce blue eyes.

According to the author of The Genetics of Eye Color, Linda Claire Guttery:

If both parents have a blue and brown gene, their eyes are brown, but if the child inherits the blue gene from each parent then the child will have blue eyes.

If, however, the child inherits only one blue gene, he or she will have brown eyes, not blue. Then again, although genetics determine someone’s eye color, other factors come into play when it comes to the actual formation of that color and its intensity, and these factors are pigmentation and melanin.

The Role of Pigmentation in Determining Eye Color

The iris contains variable amounts of pigmentation, and the amount and type of pigmentation are what chiefly determine the appearance of someone’s eye color, although that color was originally established by genetics. For instance, blue eyes contain black pigment with closely packed brownish granules, and the pigment is restricted to the back of the iris. Dark brown eyes, on the other hand, are those in which the pigment is distributed throughout the entire surface of the iris, and varying amounts and distribution of pigment produce green, gray, or hazel eyes.

How Melanin Production Affects Intensity of Color in the Eye

The more melanin contained in the iris, the darker the eye color appears, which is why some people’s eyes are darker shades and others lighter shades of the same basic color. It also explains why all newborns have blue eyes—because melanin production hasn’t yet begun, but once it does begin, babies’ eyes gradually darken, and their true eye color becomes apparent around the time they reach three.

In summary, the development of eye color is a complicated physical process but possessing at least some knowledge of that process can help people understand why their eyes are brown while other people are blue, green, gray, hazel, or perhaps even lavender like those of the still strikingly beautiful and legendary Ms. Elizabeth Taylor.

 

Demystifying the Polymerase Chain Reaction (PCR)

Polymerase chain reaction (PCR) is the process used by all those investigating DNA (deoxyribonucleic acid), from any source, to produce a sufficiently large sample for their investigation, if they only have a sample otherwise to small for their tests. This multiplication of the sample DNA is referred to as amplification.

PCR diagramFor example, forensic scientists may take a sample of DNA from a potential suspect by wiping a squib inside their mouth.

Although this in itself is insufficient for testing purposes, they will use PCR to multiply this sample many times, giving themselves a sufficiently large sample without inconveniencing the DNA donor. Without this process, they would be scraping the inside of the mouth bare or taking half the possible suspect’s blood to enable them to perform their tests.

The term is divided into two parts, “polymerase” and “chain reaction.” The word “polymerase” describes a particular class of enzyme; the “-use” suffix simply indicates that it is an enzyme while “polymer” indicates that it acts to form a chain of organic molecules.

The polymerase used in standard PCR is a DNA-polymerase; it acts to create polymers of deoxyribonucleic acid. All living organisms have DNA-polymerases; they are necessary to enable cells to divide. The polymerase used in PCR is called TAQ polymerase because it comes from an extremophile prokaryote called Thermus aquaticus. It is a type of bacteria classified under the taxonomic classification system as a member of the domain Archaea. Archaea and Eubacteria are separated into two different domains because there are very large differences between them genetically, although both are prokaryotes. The third domain in the taxonomic system is eukaryotes; these have a more complex cell structure; all plants and animals, including humans, are eukaryotes.

The “chain reaction” portion of the term signifies that the chemical reaction is ongoing as long as the process continues. Most people are familiar with the concept of “chain reaction” about nuclear reactions, where the fission of one atom triggers the fission of those around it. The meaning is essentially the same. Each cycle of the PCR process doubles the amount of DNA so that in quite a short time you can have an abundance of identical DNA from what may be a very small sample initially.

The process used is quite simple and elegant, which is why it has become such a standard tool for all those involved in a genetic examination.

Inbreeding Might Trigger Genetic Disorders

Inbreeding is the mating of closely related individuals. Inbreeding not only affects populations in nature but also has significant consequences for human populations. While the effects of inbreeding are decreasing in today’s mobile human world, in naturally occurring populations inbreeding is still easily possible.

Additionally, human society has encouraged inbreeding in some popular domesticated species like cats and dogs. The stigma inbreeding carries in modern culture is due both to commonly held moral beliefs and the higher probability of detrimental genetic disorders and diseases being passed on to successive generations.

Inbreeding Decreases Genetic Diversity

Basic genetics states that traits are hereditary. In other words, characteristics are passed from parent to offspring. Typically, if both parents have the same trait (ex. blue eyes, brown hair, connected earlobes) the likelihood of their offspring having that trait increases. In populations with a high amount of inbreeding, traits will become gradually more common. If this trait is beneficial, the population will likely continue to use it to their evolutionary advantage. However, inbred traits are generally detrimental to populations because these lower survivability and fertility. With shorter lifespans and fewer successful births, the population will either remain at dangerously low numbers or die.

Genetic diversity promotes survival. Although it is important to note situations during which inbred traits can momentarily promote the survivability of a species, populations cannot evolve or adapt to new conditions easily without diversity. Genetic diversity protects against populations succumbing to changing environments and various diseases and disorders.

How Inbreeding Increases Genetic Diseases and Disorders

Genetic diseases and disorders are often caused by recessive genes. These genes do not necessarily cause harmful traits in offspring. Instead, they are labeled recessive because both parents (the sperm and egg) must pass on the trait for the offspring to show the trait. In contrast, traits which only have to be passed on to offspring by one parent in order to be displayed are called dominant. Traits are not always outwardly physical like hair and skin color. They can also be developmental like weak hip joints or vision issues.

Cheetah inbreeding in Africa threatens its speciesDuring inbreeding, two closely related individuals who mate have a much higher chance of passing on the same recessive traits. Since these traits are often associated with harmful diseases or disorders, offspring from inbred mating have greater chances of living with debilitating issues

The Consequences of Inbreeding in the African Cheetah

Smaller, more crowded populations have higher percentages of inbreeding. The cheetah of Africa has seen several genetic bottlenecks during the history of its species. Having endured the Ice Age 10,000 years ago, decreasing suitable habitat, and the intense hunting of nineteenth-century farmers and game hunters, the cheetah, has very low genetic diversity in small populations across Africa’s nature preserves. With centuries of inbreeding, the Cheetah’s genetic diversity resembles that of a lab rat whose genetic uniformity is important to experimental science.

The potential for disease in cheetah populations is an imminent threat to the survival of the species. To offset the low genetic diversity and crowded conditions, conservationists are implementing captive breeding programs to ensure healthy offspring. Successful programs will need to mate cheetahs from different populations and promote genetic diversity which will ensure the cheetah adaptability to changing climates and human demands.

The Roles of Epigenetics in Heredity and Normal Functioning

he genetic code of each and every individual organism can tell a lot about its ancestors, some basic characteristics, and biases toward potential diseases. However, there are differences between individuals and species that are not recorded in the 4-letter genetic code but its packaging and handling. Epigenetics is defined as any factor influencing gene expression. Epigenetic mechanisms are important for normal function while their malfunction may lead to several diseases including cancer. They also take place in heredity and might be used to endow acquired traits.

Epigenetic Mechanisms

The DNA an organism carries encodes for all the proteins needed in any tissue at any time (and some nonprotein coding genes). The expression of each gene should be tightly regulated in time and space in order for a specific cell and the entire organism to function. Mutations in the genes or the factors controlling their regulation might lead to malfunctioning. For an instance, Prader-Willi syndrome is caused by genetic and epigenetic errors to the same part of chromosome 15. Every internal factor determining the gene expression profile can be considered as an epigenetic mechanism, two of which, DNA methylation and histone modifications, are the major ones.

DNA methylation is a modification in which a small molecule is attached to the DNA bases, usually Cytosine ones. DNA methylation occurs in all vertebrates, as far as scientists know. The modification silences the expression of the genes near the modification site leading to differential gene expression.

Another mechanism utilizes the histones to exert its function. The DNA should be tightly packed to fit into the nucleus. A set of proteins called histones does the packaging. These proteins wrap DNA around them and interlink to stabilize the packaging. The histones can be modified by the addition of an acetyl or methyl group to their tails. Different modifications lead to different levels of DNA accessibility around the histones and its overall expression levels. Histones modifications are sometimes used to force a specific gene expression profile in a certain tissue or at a certain time.

DNA Methylation and Heredity

DNA methylation is pre-set but can be changed during life hence adaptation to the environment can be achieved using this mechanism. The methylation pattern is changed throughout life but these changes are not transferred to the offspring. During embryogenesis, there are proteins that delete all the acquired methylation and remethylate the DNA in predefined positions. In some cases, however, the parental methylation is kept, allowing the heredity of acquired traits. Endowing acquired phenotypes using methylation supports Lamarck’s evolution theory.

Epigenetic mechanisms from gene to proteinOne example of such a process was observed in inheritance of coat color in mice (‘Epigenetic inheritance at the agouti locus in the mouse’ by Hugh D. Morgan et al. published in 1999(23) issue of Nature genetics) where mothers carrying the same genetic code had varying coat colors and endowed this phenotype to their young. It was observed that DNA methylation pattern of a specific locus differentiated between mice with different coat colors and as a conclusion DNA methylation was thought to take part in this epigenetic inheritance.

However, in a later report (‘Dynamic Reprogramming of DNA Methylation at an pigenetically Sensitive Allele in Mice’ by Marnie Blewitt et al., April 2006, PLoS Genetics) it was found that the methylation in the differentially methylated DNA is cleared during embryogenesis and the DNA is being remethylated, later on, suggesting that, at least in this case, epigenetic inheritance is not mediated by DNA methylation.

Epigenetics and Cancer

Although cancer is considered to be a genetic disease, some tumors have a normal genetic code but a disturbed epigenetic one. Research headed by Jorg Ellinger and published in September 2009 in the journal The Prostate entitled ‘Global levels of histone modifications predict prostate cancer recurrence’ finds that prostate cancer cells have much less modified histones compared to normal cells.

Occasional, unwanted epigenetic changes can cause cancer. Research published on August 2008 in the Mammalian Genome journal by Nicola Valeri et al. entitled ‘Epigenetics, miRNAs, and human cancer: a new chapter in human gene regulation’, introduces a mechanism for tumorigenesis based on epigenetic changes alone. The described model involves miRNA. Altering the modifications on the histones can generate cancer or participate in the overall cancerous effect.

DNA carries the code shaping an organism and an individual, but this code is not complete without the epigenetic one. Modifications related to DNA expression and packaging can alter the organism’s phenotype, taking a crucial role in the evolutionary process. The epigenetic code can be changed and endowed to the offspring, in oppose to the stable genetic one. Epigenetic inheritance can enable the heredity of acquired phenotypes. This kind of inheritance could be considered as a modern version of Lamarck’s Idea.

Genetic Vision Disorder Colorblindedness Treatment Breakthroughs

Genetic researchers at the University of Washington, Seattle and the University of Florida have for the first time managed to restore normal color vision in primates. Two squirrel monkeys have, for over ten years now, been trained to identify differing color groups on a touch-screen computer. Following innovative genetic therapy, they are now able to identify spectra that had previously been invisible due to their inherent red/green color deficiency.

3 types of colorblindednessWhat is Colorblindness?

Colorblindness is an inherited genetic disorder that affects the way the retina interprets different frequencies within the color spectrum. Light sensitive cones (macula) located at the center of the retina are responsible for correctly allocating these wavelengths with the appropriate color distinction. In the case of colorblindness, the genetic formula being fed to these receptors is tainted, thus causing the cones to misinterpret the varying wavelengths of incoming light. For example, sufferers of red-green color blindness cannot distinguish between colors in the green-red-yellow part of the spectrum.

Genetic Therapy Remodels Cone Receptors

The objective behind the new treatment was to develop a process whereby ‘corrective’ genetic material could be safely transferred into the retina’s defective cone receptors. This was achieved by injecting a harmless modified adeno-associated virus directly into the retina. The virus seeks to introduce a protein, long-wavelength opsin, whose specific task is the creation of red/green sensitive pigments. It is also of interest that the study is already foreshadowing practical clinical application with an eye to the future: human DNA was used in the trial negating the future need to switch genetic base material.

Procedure Ripe for Human Application

For some 20 weeks following the initial introduction of the protein nothing happened, then the turning point. The two squirrel monkeys used in the study began to recognize the red/green spectrum that is naturally missing in their particular breed. They have now steadily maintained their new color range capabilities for over two years, without exhibiting any undue side effects. It is of enormous importance that the process was successful in adult test subjects; this suggests that the brain has a far more flexible capability to ‘retrain’ itself than first thought.

One of the studies co-authors, Jay Neitz, Ph.D., a professor of ophthalmology at the University of Washington, is optimistic about the results.

Other Vision Disorders Set to Benefit from Further Development

It is commonplace for colorblindness to be considered a relatively non-debilitating vision disorder, its symptoms paling in the face of more extreme ailments. But this is of scant comfort to the many millions who live their lives within a universe of alternate hue. Those whose teachers may as well be writing lessons with invisible chalk, whose career options are stunted by the fact that they cannot distinguish various navigation lights and signals. This is a world where the subtle color whims of the masters or the diverse pallets offered by the worlds of film and fashion mean nothing; a world where sufferers are literally not getting the full picture.

Again, all this may seem paltry against disorders that induce varying degrees of true vision loss; but the color deficient are potentially not the only ones set to gain from this new treatment. As with many breakthroughs, there is potential here for a vast application. Colorblindness may be the starting point, but already disorders such as age-related macular degeneration and diabetic retinopathy are being mentioned as possible future beneficiaries.

Understanding Genetic Testing in Healthcare

Testing is used to diagnose or determine the likelihood of, genetic-related health problems. For example, a pregnant woman may undergo a prenatal test to determine if her unborn child will likely develop a disorder. People usually have a genetic consultation to provide support and information, which sometimes includes guidance on testing.

Gene, Chromosomal and Biochemical Tests

Genetic testing usually requires a blood or tissue sample. It is split into three groups:

  • Gene tests. These tests look at DNA for potential problems, such as missing or overly active genes.
  • Chromosomal tests. These tests look for problems with the number and structures of chromosomes.
  • Biochemical tests. These tests look at the actions of certain proteins, which in turn can detect problems with genes.

Types of Genetic Testing Available

  • Diagnostic – these tests are carried out when there is a reason to believe someone already has (or is at risk to) a health problem.
  • Predictive and pre-symptomatic – these tests determine whether or not someone is at increased risk of developing a health problem.
  • Carrier – these tests show if a person is carrying genes for a health problem that, while not affecting themselves, could be passed on to their offspring.
  • Pre-implantation – these tests are carried out on embryos to check for potential fetal problems.
  • Prenatal – these tests are carried out on some pregnant women to determine genetic-health issues in a fetus.
  • Newborn – these tests are carried out on newborn babies to determine any genetic health issues.
  • Pharmacogenetic – these tests determine the influences on drug interventions on the genomes of individuals.
  • Research – where testing is used to forward research in the field of genetics.

Genetic testing is not always health-related, for example, DNA testing is used in exploring ancestry. Sometimes genetic testing is carried out direct-to-consumer, where the individual takes a sample themselves and sends it back to the service, usually without intervention from a healthcare worker.

Breaking the Myths Behind DNA Research

DNA research, in itself, is neither good nor bad. It’s a tool. It’s like asking if a hammer is good or bad. A hammer is good for pounding in nails, and bad drilling in screws. Nevertheless, I think we can agree that having the option to use a hammer if the solution to a problem calls for a hammer is a good thing. The same can be said about DNA research.

Jellyfish with Green Fluorescent ProteinPossibilities in Neuroscience

In neuroscience, for example, we can take a segment of DNA coding for a gene, let’s say a green fluorescent protein (GFP) produced in nature by a jellyfish, and transfect this plasmid into cultured neurons. The neuron will start expressing GFP, and we can then see it under a fluorescent lamp under a microscope and see a living neuron in its entirety. We can watch it grow and change under different drug conditions and learn a great deal in basic research about the fundamentals of how neurons function. In cell cultures, we can even transfect DNA sequences to raise the expression of molecules, ion channels, for example, to learn more about how those ion channels work.

A common way of studying molecules in cell culture is to knock out the molecule entirely or to overexpress it, both of which are techniques involving DNA research. Even in creating transgenic lines of mice we can study glowing cells or over-expressed or knocked out molecules, all made possible because of our understanding of how DNA functions in the body.

Moving Forward with Biotechnology

DNA gets transcribed into mRNA and tRNA translates the code replicated in mRNA into amino acids and proteins are produced. RNA interference (RNAi) takes advantage of an innate molecule called the DICER complex which degrades mRNA before it can be read as a template for creating more protein. RNAi is a way we have of knocking down endogenous genes and our ability to use this technique is due to DNA research. It takes advantage of a natural process and allows us to study proteins expressed in cell cultures that we wouldn’t otherwise be able to knock down. This is a fundamental technique used in different fields of study. This simple concept alone, based on previous DNA research allows us to learn more about infinite biological processes than we otherwise would. Again, it’s a tool. It’s a very powerful tool, and it’s good to have the option to use it.

We have already made significant breakthroughs taking advantage of simple concepts like how bacteria can replicate DNA and even produce proteins from it. Insulin for diabetics, for example, is produced by prokaryotes because of DNA transfection techniques.

If gene therapy turns out to be a cure for cancer or perhaps, more straightforwardly, a cure for Fragile-X syndrome or congenital heart defects, how can we even consider turning a blind eye to such a positive possibility? It’s up to us not to use research of any kind, DNA-based or otherwise, for harm. DNA research can do so much good. It already has.

Direct Shell (SSH)

DIAG has several ways in which users can interact with it in order to gain access to a best-in-class academic computing grid. Among these are “cloud” type resources, provided by the Nimbus framework; Ergatis, for building pipelines and workflows and executing them via a simple yet powerful web interface.

However, researchers frequently need a simple way to experiment with their code and data before scaling them up for use on large scale systems. Many scientists find having an easy and direct way of opening a shell with a simple login prompt to be an invaluable way to prototype and test their code. DIAG provides just such a mechanism. If you are interested in having “shell” access to DIAG computing infrastructure, be sure to add it to your selected access methods when you register for an account.