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Proteomics/Protein Separations - Centrifugation/How the Centrifuge Works

Centripetal Force
A works by spinning mixtures around a central axis (centrifugal force). As the sample spins the tendency of the of the object is to move in a straight-line path. However, due to its confinement within the centrifuge, the path of the object must be bent into a circular one. The body of the centrifuge, or the body of the container within the centrifuge, provides a normal force that pushes the object toward the center of the circular path of travel. This inward force is referred to as a, and its magnitude and direction are exactly what is needed to keep the object moving in a circular path around the axis of rotation of the centrifuge.

Centrifugal Force
The strength of the outward force exerted by an object (due to its inertia trying to move it in a straight-line path) as it moves in a circle at a constant angular velocity depends on the angular velocity and the radius of rotation. This force is denoted F, the angular velocity is measured in radians and denoted as w, and the radius of rotation, r, is measured in centimeters.

$$F = mw^2r$$

Usually, the value cited for the force applied to a suspension of particles during the centrifugation is a relative one, that is to say it is compared with the force that the earth's gravity would have on the same particles. This is referred to as relative centrifugal force (RCF). It was Galileo Galilei (1564-1642) who first systematically and scientifically investigated gravity as a natural phenomenon. The gravitational acceleration constant is customarily assigned the symbol "g" and for simplicity taken to be 9.80 m/sec sec. Based on this measure, relative centrifugal force is expressed as:

$$RCF = mw^2r/9.80$$       (RFC = F centrifugation / F gravity)

The common way of denoting the operating speed of a centrifuge is in “revolutions per minute” or rpm. The formula above may be converted so that this relationship expressed as such. If you are expressing the radius in cm then the formula for RCF is:

$$RCF = 11.17r (RPM/1000)^2$$

If you are expressing the radius in inches then the formula for RCF is:

$$RCF = 28.38r (RPM/1000)^2$$

The centrifugal force created by the spinning of the centrifuge is greater at the bottom of the tube (away from the central axis) and less at the top of the tube (closer to the central axis). This difference is almost twofold. Because denser items have a greater mass, this causes their centripetal force to be greater (F=ma), and the overall result is that they settle near the outside of the circular path. This places denser objects at the bottom of a test tube that has been run in a centrifuge. Less dense objects remain closer to the center of the path, or the top of a test tube that has been run in a centrifuge.

The Action of Centrifugal Force on Molecules
As samples spin in a centrifuge the particles in each sample are subjected to centrifugal force. However, this force is proportional to the mass of the particle. To express the centrifugal force applied to a particular molecule its molecular weight (M) is used in the formula:

Centrifugal force = $$Mw^2r$$ Because weight takes into account the force of gravity, using molecular weight in the formula for centrifugal force removes the need to divide by the force of gravity as shown above. This formula shows how particles within a centrifuge are separated based on their molecular weight. In addition to this the size and shape of a particle also affects its migration in the gradient created by centrifugation. For example, plasmid DNA will travel farther down a gradient then chromosomal DNA. This is the result of the counteracting forces of buoyancy and friction counteracting the force of centrifugation.

Buoyancy and Friction
While the centrifugal force acts to accelerate a particle away from the axis of rotation, the particle is also subjected to additional forces including the force of buoyancy and the force of friction. Buoyant force = Mω2rVρ
 * Buoyancy force refers to the interaction of the molecule within the solvent. It is calculated as the centrifugal force multiplied by the volume of solvent the molecule displaces (V, the “partial specific volume”) and by the density of the solvent itself (rho – r).  Together this gives the formula:

Frictional force = f(v) = f(dr/dt) The final result of these forces acting together is that a particle will move through the solvent, away from the axis of rotation, until the centrifugal force is equivalent to the forced of buoyancy and friction. Using the formulas above the sedimentation coefficient (s) can be calculated from the molecular weight of a particle. Sedimentation Coefficient (s) = M(1-Vr)D/RT (R is equal to the gas constant   T is equal to absolute temperature) The sedimentation coefficient of a molecule describes where it will settle in a gradient with the viscosity and density of water under centrifugation and is measured in seconds. For biological molecules these values range between 1 – 500 x$$10^{-13}$$ seconds. Instead of using $$10^{-13}$$, this number is described as one Svedberg unit (S) after Theodore Svedberg; so that 12x$$10^{-13}$$ is expressed as 12S.
 * As the particles move through the solvent frictional force is also generated. The size and shape of a molecule are determinates in the measure of this force.  These contribute to the rate of sedimentation which is expressed as the change in the axis of rotation over time (dr/dt).  This force combines with the Buoyant force to counteract against the centrifugal force.

Coriolis Force
In addition to centrifugal force, particles in suspension (and the body of suspending fluid itself) within a spinning rotor are subjected to Coriolis force. The Coriolis force which results from the inertia of the liquid and the suspended particles, is a small force directed at the right angles to both the axis of rotation clockwise. This force acts to deflect particles in a counterclockwise direction (and vice versa). Under nearly all experiment conditions, the coriolis force is very small in comparison with the centripetal force; however, its effects are magnified when the rotor's speed changes (e.g during acceleration and deceleration). While the centrifugal force acts to accelerate a particle away from the axis of rotation, the particle is also subjected to additional forces including frictional force, the force of buoyancy and gravitational force.

Centrifuge – the Machine
The basic design of a centrifuge consists of a rotor which holds samples together rotates around a fixed axis driven by a motor (in modern centrifuges). More advanced centrifuges may also have lubrication and cooling systems. In addition to this, some centrifuges are capable of creating a vacuum environment around the rotor.

Rotors

The most popular and widely used centrifuge rotors are the swinging-bucket and fixed-angle rotors. Two other types of rotors are the vertical rotor and the zonal rotor.

 * Fixed-angle (or angle head) rotors are generally simpler in design than are swinging-bucket rotors. In this type of rotor, the centrifuge tubes are held at a specific and constant angle to the horizontal plane that is the tube does not reorient between the vertical and horizontal positions. This type of rotor works very well for simple pelleting centrifugation but has limited and variable success in rate-zonal sedimentation and isopycnic sedimentation respectively.

Most swinging-bucket rotors are interchangeable so that different size test tubes can be used. Additionally, some have the ability to hold multiple test tubes in a single arm.
 * Swinging-bucket rotors are able to pivot within the centrifuge. As speeds increase the angle of the rotor perpendicular to the axis of rotation also increases, positing it in a horizontal configuration.  Conversely, as the centrifuge slows down the rotor returns to a vertical position.  When the bucket swings out the pathlength is increased allowing for improved separation of individual particles, particularly in density gradient centrifugation.  This type of rotor is inefficient when used for pelleting.  However, it is good for use with both rate-zonal and isopycnic sedimentation.

 * Vertical rotors hold samples in a vertical position within the centrifuge. This type of rotor is not suitable for pelleting centrifugation but it does a good job when used for rate-zonal sedimentation, and an excellent job with isopycnic sedimentation.

Centrifuge Tubes
Depending on the sample/ rotor size and speed of centrifugation different types of centrifuge tubes can be used. Proper selection of centrifuge tubes helps to ensure that leakage does not occur and none of the sample is lost, the chemical properties of the sample and the tube do not conflict, and that the sample can be recovered with little effort.

Rotor and Tube Materials
Early rotors such as the Svedberg rotors were made of steel and occasionally brass. The high density of these materials and the resulting high rotor weight produces an appreciable load on the centrifuge drive and significantly limits operating speeds. Most commercial rotors are now made of the partly or entirely of aluminum or titanium.

Lubrication and Cooling Systems
The high speeds at which centrifuges operate generate a great deal of frictional force. Along with this friction comes heat. To prevent damage to the centrifuge and/or samples within the centrifuge, many present day centrifuges have lubrication and cooling systems to combat friction and the heat it produces.

Convection occurs whenever uniform suspensions of particles are sedimented in a conventional centrifuge. The term "convection" means the bulk movement of solute and/or solvent within the centrifuge tube. Unwanted convection can be caused by variations in temperature in different parts of the centrifuge. By controlling the temperature, lubrication and cooling systems help to guard against this.

Superspeed vs. Ultraspeed Centrifuges
There are two basic types of preparative centrifuges; superspeed centrifuges and ultraspeed centrifuges or ultracentrifuges.

 * Superspeed centrifuges generally operate at speeds up to about 20,000 rpm. These centrifuges usually do not require evacuation of the rotor chamber, and drive the rotor directly to through belts or gears.  The picture below is of a Sorvall RC-5B refrigerated superspeed centrifuge.

 * Ultracentrifuges can be operated at much greater speeds (up to 65,000 or 75,000 rpm). Due to these high speeds the rotor chamber must be evacuated of air to reduce friction and permit accurate rotor temperature control. In most ultracentrifuges the rotor is driven either by a motor and a set of gears or by an oil or air turbine system. the picture below is of a Beckman Coulter optima LE-80K ultracentrifuge.

Next section: Density Gradient Centrifugation


text:
Talk:Proteomics/Protein Separations - Centrifugation/History of the Centrifuge

Slight type that needs to be corrected on svedberg picture. -Jfb4497

This account seems to contain some incorrect statements. As far as I've been able to find, centrifuges have been used since the mid 1800s, not the mid 1400s. Moreover, Friedrich Miescher did not use a centrifuge to isolate nucleic acids. See the following excerpt on the work of Miescher from "DNA pioneers and their legacy" quoted on http://www.fmi.ch/members/marilyn.vaccaro/ewww/dna.pioneer.excerpt.htm

"After filtration to get rid of tissue fibers, the cells were left to sediment to the bottom of the beaker; laboratory centrifuges were nonexistent in those days. When examined in the microscope, the leucocytes seemed intact and showed no sign of damage."

-Lvzon

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
User:Sir Isaac

My name is Randy Kirk

title: User:Sir Isaac


text:
Wikijunior:Human Body/Heart

What does a heart look like?
The heart is about the size of a person's clenched fist. It is made of muscle. It is a muscular organ.

What are the parts of the heart?
The heart has two sides: the left side and the right side. Each side of the heart is divided into two parts, called the atrium and the ventricle. The atrium is the top part. The ventricle is on the bottom.

Both sides of the heart have a blood vessel (a vein) through which blood flows into the atrium. Valves are like doors that control where blood goes. Valves separate the atrium from the ventricle. Another set of valves controls the flow of blood from the ventricle to the artery that sends blood back into the body.

The heart is a big muscle that builds up blood pressure by contracting. When the heart contracts, it squeezes or pumps blood throughout the entire body. This is the "beating" of your heart.

Right heart
The vein leading to the right atrium is called vena cava'. It has the blood returning from all parts of the body (without oxygen). The right ventricle pumps the blood through the pulmonary artery to the lungs to get oxygen. Veins bring blood to the heart.

Left heart
Blood with fresh oxygen returns from the lungs through the pulmonary vein and flows into the left atrium. The left ventricle pumps the blood into the artery called the aorta. It supplies the whole body except the lungs with blood.

What is the function of the heart?
The heart is the strongest muscle in the body. The heart is a pump that pumps blood to different organs of the body.

Blood is the medium that carries gases, liquids, nutrients, and waste all over the body. It is red in color because of the red blood cells. Blood also contains white blood cells which defends the body against diseases and makes repairs to damaged tissues.

The heart moves the blood (with the oxygen, nutrients, water, and waste) to and from all parts of the body.

How does the heart beat?
Before each beat, your heart fills with blood. Then its muscle contracts to squirt the blood along. When the heart contracts, it squeezes — try squeezing your hand into a fist. That is like what your heart does so it can squirt out the blood. Your heart does this all day and all night, all the time.

What organ system(s) is the heart connected with?
The heart is part of the circulatory system. Its main job is to move blood from the lungs to all other parts of the body and back. In the lungs, the blood gets oxygen from the air you breathe and leaves waste to be breathed out.

How does the heart interact with other parts of the body?
Blood with fresh oxygen is pumped through the body through tubes called arteries. Arteries divide up into smaller and smaller blood vessels. Finally, tiny blood vessels called capillaries deliver oxygen and nutrients to the body's cells. Then carbon dioxide and waste products are absorbed in the blood. The blood then returns to the right heart through blood vessels called veins. From the right heart, blood is pumped through the lungs where carbon dioxide is released and oxygen is absorbed to re-oxygenate the blood. From the lungs, the blood returns to the left heart where the cycle begins all over.

Note:
 * Blood vessels leaving the heart are called arteries. (You can remember this by thinking of "a" for "away" from the heart.)
 * Blood vessels entering the heart are called veins.
 * All arteries contain oxygenated blood except the pulmonary artery which sends blood to the lungs.
 * All veins contain de-oxygenated blood except the pulmonary vein which moves blood from the lungs to the left heart.

How can you keep your heart healthy?
You can have a healthy heart by:
 * getting appropriate exercise
 * eating healthy food (a balanced diet)
 * controlling high blood pressure
 * controlling how much you smoke

title: Wikijunior:Human Body/Heart


text:
Biblical Studies/New Testament Commentaries/The Gospel of John/Chapter 16

Chapter 16: Verses 1-4
In the beginning of this chapter, Jesus warns his disciples that they can expect much persecution. He does this to keep his disciples from having unrealistic expectations. His advanced warning is intended to keep his followers from questioning their faith when things start to happen and, most of all, to keep defections at a minimum (Smith 291). "They will put you out of the synagogue; in fact, a time is coming when anyone who kills you will think he is offering a service to God" (John 16:2). "Ejection from synagogues was a significant threat intended to discourage belief in Jesus as the Messiah" (291). The power behind such an ejection was communal. The synagogue was a very important form of community organization that was paramount to Jewish social and public life. To be effectively cast-out of your own synagogue represented therein an ejection from the community. After relating the cruel and harsh reality that was to come, Jesus reminds his disciples that his coming absence is reason enough for this warning. Jesus is once again foreshadowing his coming death at the hands of the Jewish authorities.

Jesus foretells to the disciples what will happen to them after the Romans decide the Christians are a threat and the Jews reject them from the synagogue. He tells them about the persecutions they will face in the future and the pain they will endure for their faith in him.

==Chapter 16: Verses 5-16 (The Work of The Paraclete (a pneuma/angel different from the pneuma/angel that was in Jesus. The angel in Jesus was the angel of Wisdom. The angel for believers is called the angel of the Truth.)== In this portion of John Chapter 16, Jesus describes the work of the paraclete; The "Spirit of the Truth." First, Jesus addresses the question the disciples have not asked: Where is Jesus going?  The peculiarity of this remark comes with a glance back to Chapter 14, where Peter has already asked this very question.  Could the text be read in a different arrangement?   Jesus goes on to answer his own question, saying that he will be with the Father.  He says this to console them in their grief at his leaving, also, in his stead he promises   consolation through the Spirit of the Truth.  The Spirit of the Truth has a mission to help followers remember all the words Jesus spoke, to teach them the meaning of the parables and difficult sayings he spoke, to clarify the prophecies of his return,  to help them understand the doctrines of sin, and righteousnes and give them a right understanding of Satan and his ongoing destruction. This spirit cannot be God or a third person in God for it has severe limitations. It is not allowed to speak its own thoughts, but only what it hears. It is merely a messenger (agellos-angel)

Essentially, the spirit of the truth may be regarded as a conduit to God's enlightenment of believers, who will then enlighten the world. In 16:12-13, Jesus says, "I still have many things to say to you, but you cannot bear them (comprehend them) now. When the Spirit of the Truth comes, he will guide you into all the truth (that Jesus taught)." These verses identify the Paraclete as the medium of those encounters. In verse 16, Jesus has used the expression "a little while" to speak of his departure which limits his time in the present (referring to the time leading up to Jesus' death). "A little while" in the farewell discourse also seems to refer to the time between Jesus' death and his resurrection.

Jerome translated Paraclet as advocate. However, the paraclete is not a defense lawyer but a prosecutor, so advocate is not the correct word. It convicts the world of sin, so comforter is also not the right word.

Some try to say that it is the return of Jesus in spirit form but that would make verses 13, 14 and 15 quite confusing if you see the paraclete as "surrogate for Jesus himself." The paraclete is a pneuma/angel sent to illuminate the words of Jesus. Just as Jesus received a pneuma at his baptism to help him, all believers who ask for it will receive the paraclete to help them.

Verses 13-15 state, "When the Spirit of the truth comes, he will guide you into all the truth (taught by Jesus); for he will not speak on his own, but will speak whatever he hears, and he will declare to you the things that are to come (the return of Jesus not a road map of the future). He will glorify me, because he will take what is mine and declare it to you.  All that the Father has is mine.  For this reason I said that he will take what is mine and declare it to you." If the Spirit is able to "speak whatever he hears," he is a separate entity from Jesus.

Another interesting characteristic of verse 14 and 15 is this idea of the Spirit "declaring" things to the disciples. It is not entirely clear just how this declaration will come about or what form it is to take. However, as D. Moody Smith points out in his commentary on John, there are some suggestions found elsewhere in the New Testament that might shed some light on the mystery. In 1 John 4:1-3 you have a christological test to determine false spirits from true ones, "1 Dear friends, do not believe every spirit, but test the spirits to see whether they are from God, because many false prophets have gone out into the world. 2 This is how you can recognize a Spirit from God: Every spirit that acknowledges that Jesus the messiah was real human is from God, 3 but every spirit that does not acknowledge that is not from God.

This is the spirit of the antichrist, which you have heard is coming and even now is already in the world."

To say that Jesus was God in the flesh means Jesus was not a real man like all other men. Or to say he pre-existed means he is not a like all other men.

To say he was human you must agree he was 100% human with nothing extra. If you add anything to his humanness or take away anything you are teaching the anti-christ doctrines of the Gnostics who said he was man but more than man. Some even say he only appeared to be a man. He only had the "likeness" of human flesh.

Chapter 16: Verses 17-33 (The Disciples' Grief will Turn to Joy)
At the very end of chapter 16 Jesus proclaims to his disciples that an hour is coming where his disciples will all leave and go there own ways, leaving him undoubtedly and utterly alone. Yet Christ is never alone because the Father is with him, and he tells the disciples all this that when they find themselves all alone and without him, they can turn and find him in spirit. There will be much suffering in the world but He will get them through it, like always.

You believe at last! Christ's words to his disciples in verse 31 raise an interesting point: exactly what does it take for humanity to believe at last? Christ's disciples had been with Him for the duration of his ministry, and were personal witnesses to many of His miracles. If these men could not readily accept him, how have many circles of modern Christianity become so "unwavering" in their beliefs? These circles, which are ironically the most bibliocentric, seem to ignore the doubt and fear evidenced by the Apostles in the Gospels. This doubt is glazed over in an attempt to assert that these men were rigorously faithful, warping an essential cornerstone of Christianity (that is, doubt) into blind faith. How has this proven detrimental to spreading the message of Christ in the modern world?

Jesus' death and resurrection foretold?

Many believe that in verses 16-19 Jesus is speaking to the disciples about his up and coming death and resurrection. This idea would correlate with one of the reoccurring themes in John of Jesus trying to explain to His disciples what was to come. For instance verse 16 states: "A little while, and you will no longer see Me; and again a little while, and you will see Me." (NAS) this verse looks very similar to previous verses in the gospel of John. In John 7:33 there is a distinct resemblance in message "Therefore Jesus said, "For a little while longer I am with you, then I go to Him who sent Me." (NAS) Jesus continually tries to get His disciples to believe in these things He says by performing His many works, but they still do not understand. Jesus has continued to foretell to the disciples of His upcoming death and resurrection in John 12:35, 13:33, and 14:19.

Verse 17 states: "Some of His disciples then said to one another, "What is this thing He is telling us, 'A little while, and you will not see Me; and again a little while, and you will see Me'; and, 'because I go to the Father'?" (NAS) This verse reiterates verse 5 in the beginning of this chapter where Jesus says: "But now I am going to Him who sent Me; and none of you asks Me, 'Where are You going?'" (NAS) Jesus tries to explain where He is going in previous chapters of John as well. For instance, look in John 7:33, 14:12, and 16:10.

Lastly in verses 18 and 19 it says: "So they were saying, "What is this that He says, 'A little while'? We do not know what He is talking about. Jesus knew that they wished to question Him, and He said to them, "Are you deliberating together about this, that I said, 'A little while, and you will not see Me, and again a little while, and you will see Me'?" (NAS) The disciples still needed some type of validation to understand what Christ was trying to say. This questioning and confusion parallels their confusion in John 6:61 and also in Mark 9:32.

Even with these parallels in scripture, some also believe that these passages could be a foretelling of the second coming of Christ. To some, this notion seems evident in previous gospels. However, this idea would not precisely fit with the gospel of John since one of the major focuses of this chapter is of Jesus’ teachings and foretelling of His death and resurrection not of the second coming. It is also likely that Jesus is referring to his resurrection because of the time in which John was written, most likely the latest of the Gospels; a time when the expectations of the 2nd coming were wearing thin, and Christianity had to (in some ways) move away from its eschatological theology.

There are two changes in the relationship between the disciples and Jesus that will be a basis of joy for them. The first change is reflected in their no longer needing to ask Jesus questions (v. 23). The stuff the disciples have been asking about will become clear once they see the Lord's death and resurrection and receive the help of the Paraclete. The disciples will have an understanding of Jesus when the Father sends them the spirit/angel of the truth. The second change will be their sharing in Jesus' work as his friends (vv. 23-24). This is the truth behind Jesus' reference to asking the Father in his name (cf. 14:13; 15:7). They have not asked in his name up to this point because they have not dwelt in him and he has not dwelt in them. This will soon change, and then they will share in the eternal life that Jesus has with the Father (Gospel Communications, 2007).


text:
User talk:Gknair~enwikibooks

srilanka allot the tamil peoples land for separate nation.

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title: User talk:Gknair~enwikibooks


text:
User talk:Ahadland123~enwikibooks

Hello, and welcome to Wikibooks!

Here are some tips to help you get started:
 * To learn the wiki-markup-language syntax, see Help:Editing.
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 * Remember to conduct any editing experiments in the sandbox.
 * You can tell the community something about yourself in your userpage.
 * You can get to this page by clicking the tab at the top of the page labeled with your registered username.
 * If you are a Wikipedian, see Wikibooks for Wikipedians for a primer on how things work here (it's a little different).
 * If you want to base your work here on materials from Wikipedia, please use WB:RFI (requests for importation) to bring the material over in compliance with the GFDL.
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Good luck! -- Herby talk thyme 07:06, 2 April 2007 (UTC)

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text:
Hacking

A is someone who explores methods for breaching defenses and exploiting weaknesses in a computer system or network. Hackers may be motivated by a multitude of reasons, such as profit, protest, information gathering, challenge, recreation, or evaluation of a system weaknesses as a to assist in formulating defenses against potential s. To efficiently resist s white hat hacker should think and dream like a black hat hacker. Beginner is called.

Security hacker should not to be confused with - follower of. In general hacker is not related to security. There are, , , , , , hackers and even ers and ers. The common for all kinds of hackers is that non-hackers don't understand what a hacker does.

 * Introduction
 * Recommended style conventions
 * Ethical hacking & The hacker ethic
 * Background knowledge
 * Reconnaissance
 * Cyberattack
 * Cracking wireless networks
 * Exploits
 * Penetration
 * Post exploitation
 * Tools

title: Hacking


text:
Hacking/Introduction

Hacking is the art of exploiting computers to get access to otherwise unauthorized information. The interpretation of what constitutes unauthorized access is relative to the party in question, however. Now that the world is using IT systems to gather, store and manipulate important information there is also a need to make sure that data is secure. However, no system is without its problems. Holes are often present within security systems which, if exploited, allow hackers to gain access to this otherwise restricted information. The following Wikibook aims to give you the fundamental information required to grasp a foundational understanding of what constitutes hacking and the various methodologies under which it is performed, both ethically and unethically.

Hacking and information security are continuously adapting fields and as such, the relevance of material presented in this book should be cross referenced with more timely sources to insure proper guidance.

Hacking is a controversial and divided topic, with varying interpretations of what constitutes ethical hacking. This book will attempt to maintain a neutral and unbiased presentation of fact, not favoring any one side. For a further discussion of one interpretation of "ethical hacking" see Hacker Ethic.

title: Hacking/Introduction


text:
Hacking/Introduction/The hacker ethic

It is important that hackers follow The Hacker Ethic in the same way that it is important that police follow their code of conduct. An abuse of skill within the hacking world causing harm to others. Remember: It is almost impossible to gain respect at the expense of others.

The Original Ethic
Back when computers just started to reach universities and students had access to open systems, curious users began to show a certain disregard for the rules. These users would enter areas of the system without authorization, gaining access to privileged resources. With no Internet and no copies of Hacking Exposed or Security Warrior to assist them, they had to figure out how to enter the systems on their own.

Although these young students represented the first hackers, they had no malicious intent; they simply wanted knowledge, information, a deeper understanding of the systems which they had access to. To justify and eventually distinguish their efforts, the hacking community developed The Hacker Ethic as a core part of their subculture. The Hacker Ethic states two basic principles:

 * Do no damage.
 * Make no one pay for your actions.

These two principles fall hand in hand. The original hackers had an intention to learn about the systems they invaded, not to destroy them or steal valuable confidential information. They wanted to know how they worked, their flaws, their strengths, interesting functions of their design. They had no authorization; at the time, they made up for this by making a point of neither interfering with anyone's work nor costing anyone any money in the process of exploring the system.

Unfortunately this mantra does not provide a fully effective cover for your actions. Even disregarding the legal ramifications, such as the Computer Fraud and Abuse Act of 1986, your actions will have devastating unintentional consequences if not carefully controlled. Robert Morris created the Morris Worm to gauge the size of the Internet harmlessly; unfortunately, it loaded down the systems it infected due to exponential re-infection, causing tens of millions of dollars of financial damage. You must always remember to carefully consider the short and long term impact of your actions on any system.

Today's Ethic
Today we need to add one more rule to The Hacker Ethic, a rule that we should have added long ago. The Morris Worm illustrates why this rule exists, even beyond legality.

 * Always get permission ahead of time.

Please remember to always get permission before acting. Your actions cause a major disruption to the targets you attack. Networks become slow, servers crash or hang, and you create spurious log entries. Any institution with a useful IA sector will notice your attack and panic, believing you to have malicious intent; they will invariably expend resources searching for back doors and trying to determine what confidential information you stole. All of this, even if you don't get caught, demands that you acquire permission ahead of time.

You always have authorization to hack into servers you own; likewise, if you participate in a Capture the Flag game or as Red Cell in a Red vs Blue competition, you implicitly have the right to hack into whatever you can get your hands on. In all other cases, you need to ask the owners of the machines for authorization; you can even ask them to pay for it, selling your services as penetration tests and giving them a comprehensive outline of their network's vulnerabilities and proper mitigation steps to improve their security. As long as you have permission ahead of time, and you remember the first two rules of The Hacker Ethic, you can do as you please with the network and the affected machines.

title: Hacking/Introduction/The hacker ethic


text:
Talk:Bourne Shell Scripting/Environment

Ugh!

Speaking as someone who's had to teach shell scripting I have to say that there are quite a few parts of text which I think will lead to considerable confusion.

 * The environment conflated with process state. A process' file descriptor list and signal handlers, etc, are not considered parts of the "environment." I think it's best to think of the environment specifically as the block of memory in which environment variables are stored
 * The positional arguments (represented as $1, etc.) are on the command line ... which is usually not thought of as part of the environment.
 * The environment is best described as a region of a process' memory which contains a list of name/value settings ... ASCII strings. It's used by the shell and by many of  the programs run under a shell as a way to store settings which can be specific to a process or to a family of processes.  (In other words its a way for configuration settings to be passed from a parent process to its descendents).
 * I find that it helps students understand the environment when I draw a conceptual memory map of a process ... explain the concepts of fork and execve ... and show how the execve replaces ... over-writes all of a process' memory except for the environment. This leads almost all students to an understanding of why the export command is used to shift variables and their values out of the local heap and into the environment and gives them the insight to understand why environment variables can only be "inherited" and why the cannot be modified by subshells and other sub-processes.
 * Explaining a little about the underlying, fundamental, fork/exec* model also helps the student understand the most basic command executions on a much deeper level. They learn that all normal external command execution involves a subshell which exec*s a program while their shell wait*s for it to complete.
 * As we get into more advanced topics it becomes far easier for them to master concepts such as pipes (which are, after all, an inter-process communications mechanism --- and thus inherently involve a subshell or other subprocess), the exec shell command (when used for purposes other than file descriptor manipulation), and from there the concepts in eval and source (the . command).

In other words I think that peeling away a little of abstraction layering ... and giving the students a peek at the inner workings of these things builds a solid foundation on which they can progress more confidently.

(So I need to re-write this section a bit ... but first I wanted to post it here to the discussion to here any dissenting opinions). JimD 07:53, 2 April 2007 (UTC)

title: Talk:Bourne Shell Scripting/Environment


text:
Bartending/Cocktails/Mountain Meister

The Mountain Meister is a simple mixed drink.

Ingredients

 * Mountain Dew
 * Jägermeister

Glass

 * Highball

Procedure

 * 1) Mix 1 part Jägermeister with 2 parts Mountain Dew in an 8 oz highball glass.

Variations

 * More or less Mountain Dew for taste.

Related cocktails

 * Bob Dylan

title: Bartending/Cocktails/Mountain Meister


text: Category:Cocktails with Jägermeister

title: Category:Cocktails with Jägermeister


text: Category:Cocktails with Mountain Dew

title: Category:Cocktails with Mountain Dew


text:
Wikijunior:Human Body/Glossary

Glossary
aerobic (adjective) – Using or needing oxygen or air, such as aerobic exercise that makes you breathe heavily.

aorta (noun) – The largest artery that carries oxygenated blood from heart to all parts of the body.

aqueous (adjective) – Of or related to water.

artery (noun) – A blood vessel or tube in the body that carries blood away from the heart to other parts of the body.

asthma (noun) – An illness that causes wheezing and difficulty in breathing due to blocked airways.

atrium (noun) – A chamber of the heart that take blood into the heart from the veins

bloodstream (noun) – The flow of blood throughout the body.

blood vessel (noun) – A tube that carries blood inside the body.

capillary (noun) – A very small blood vessel or tube in the body that goes between arteries and veins, carrying blood and allowing the exchange of oxygen, carbon dioxide, water, nutrients, and waste.

cardiac (adjective) – Or related to the heart

cavity (noun) – A space inside the body, such as the space the heart and lungs are in.

cell (noun) – The smallest part of a living thing that can be seen only with a microscope.

cellular respiration (noun) - The process where cells use oxygen to help generate their energy.

cholesterol (noun) – A naturally occurring chemical in the body's bloodstream that can be good or bad; too much of the bad kind can be unhealthy for the body.

circulatory (adjective) – Of or related to the system of the human body that includes the heart, arteries, veins, capillaries and blood and that carries oxygen and food to the cells through arteries and then carries away wastes.

digestion (noun) – Changing food into chemicals like sugar and protein that are small enough to get into the cells where they can be used for energy and growth.

disease (noun) – sickness; illness

esophagus (noun) – A tube in the body that is inside the neck and goes from the throat to the stomach, carrying food that is swallowed.

exercise (noun) – Physical activity done to keep the body healthy, such as running or lifting weights.

exhale (verb) – To breathe out; to blow out a breath of air.

expel (verb) – To get rid of.

germ (noun) – Tiny living things, such as bacteria, that grow very fast, duplicating themselves over and over until there are millions or billions of cells, and if harmful, can cause infections.

haemoglobin (noun) – A red iron-containing protein that occurs in the body's red blood cells and carries oxygen to all of the body's other cells.

immune (adjective) – Of or related to the system of the body that protects the body from infection and includes white blood cells, other chemicals in the blood, lymph nodes, and other organs.

inhale (verb) – To breathe in; to take in a breath of air.

liver (noun) – A major body organ that stores sugars for release when needed, makes bile to aid in digestion of fats, makes urea from protein wastes, and acts as a filter for the blood.

lobe (noun) – A rounded section of a body part, such as an ear lobe, lobes of lung, or lobes of the liver.

medication (noun) – Drugs or pills, often given by a doctor, to make the body healthy.

muscle (noun) – A type of tissue in the body that is attached to bones and that allow motion.

nutrient (noun) – A source of nourishment; something that feeds living things and is necessary for life.

organ (noun) – A distinct part of the human body that does a specific job, such as the heart, lungs, and kidneys.

oxygen (noun) – An element that is found in air and water and that humans need to breathe in order to live.

pancreas (noun) – A body organ that is part of the digestive and endocrine systems and that makes a juice which goes into the small intestine to help digest carbohydrates, proteins and fats and makes insulin.

plasma (noun) – The liquid part of blood, made up of water and dissolved proteins.

pulmonary (adjective) – Of or related to the lungs; of or related to the system of the body that gets oxygen to the blood stream and removes carbon dioxide from the blood using the windpipe, bronchial tubes, and lungs.

saliva (noun) – spit; The watery liquid found in the mouth.

system (noun) – A group of body parts that work together.

vein (noun) – A blood vessel or tube in the body that carries blood away from various parts of the body back to the heart.

ventricle (noun) – A chamber of the heart that pumps blood from the heart into the arteries to be taken to various parts of the body.

waste (noun) – The part of food that the human body can't use.

yogurt (noun) – A soft, pudding-like food made from milk that contains live bacteria that can help digestion.

title: Wikijunior:Human Body/Glossary


text:
Wikijunior:Human Body/Blood

Blood is vital for the human body. Without it, none of the other organs or cells of the body could function.

What does blood look like?
Blood is a liquid. In humans, as with many other animals, oxygenated blood (the blood that is carrying a lot of oxygen) is bright red. De-oxygenated blood (the blood that has given away most of its oxygen) is a darker shade of red. It is often thought that the blood in veins is blue, but this is not true. It only looks blue through the skin because of the way light moves through the skin.

What are the parts of the blood?
Blood is made up of many different things, red blood cells, white blood cells, platelets, and plasma. These three types of cell are very important and keep the other cells of the body alive and healthy. Also blood is used to send signals in the body since every cell can be reached this way. For example, the hormone (a small signalling molecule) insulin tells cells that food is on the way and cells should take up nutrients from the blood. This is the way of cells send each other instructions.

The red blood cells carry gases such as oxygen that are needed for cellular respiration.

The white blood cells are part of the immune system and play an active role in fighting infections in the body.

The platelets help the blood clot or stick together. If you get a cut or scrape, this helps stop the bleeding. The platelets create a 'mesh' that the red blood cells can clot upon. This prevents the body from losing more blood and helps to keep infection from entering the body.

The blood plasma is an aqueous substance made up of about 92% water, 8% blood proteins and small traces of other substances including:
 * Antibodies (for fighting off infections)
 * Hormones (chemical messengers used to control many of the body's functions)
 * Oxygen (transporting it to other cells)
 * Glucose and fats (to feed the body's cells)
 * Carbon dioxide (removed from other cells)
 * Salts (for maintaining the correct levels of ions in and around cells; when salts dissolve in water, they turn into ions)

What is the function of the blood?
In the human body, blood is the transport system. It allows the body to bring essential things such as nutrients and oxygen from central locations (i.e. The lungs or small intestine) to every part of the body. Blood is circulated all the way around the body many times a minute. It is pumped by the heart.

Transport of Oxygen
One of the most important things that the blood does is to carry oxygen from the lungs to the cells of the body. It is carried inside the red blood cells by a chemical called haemoglobin.

Transport of Carbon Dioxide
As cells function, they produce carbon dioxide. If this is left in the cells, they become useless. Fortunately, the blood removes the carbon dioxide from the cells and takes it to the lungs where it can be breathed out of the body.

Controlling Body Temperature
The blood is also used to control the temperature of the body. If the body becomes hot (during the summer for example), more blood will flow to the surface of the skin. This cools the body. If the body becomes cold, the blood will be forced to flow deeper inside the body, keeping the body warmer.

How does the blood interact with other parts of the body?
Blood is produced in the bone marrow (inside bones). It also gets parts from the liver and kidneys among other body parts.

Blood is pumped throughout the body by the heart. Blood gets oxygen from the respiratory system and nutrients from the digestive system. Blood flows through the kidneys to be cleaned.

When the blood cells have reached the end of their useful lives, they are broken down in the liver and then put into the urine by the kidneys to get rid of non-reusable parts. The reusable parts, such as protein and iron, are recycled by the liver.

title: Wikijunior:Human Body/Blood


text:
Wikijunior:Human Body/Stub Template

What do Arteries, Veins and Cappillaries look like?
Have you taken a look at your wrist recently? Well if you have, you might have noticed some faint red and blue lines running across them. The red ones are called arteries. They carry blood away from the heart and transport it to the rest of the body. Meanwhile, the blue ones are called veins and they carry blood the opposite direction to the artieries - back from the rest of the body to the heart.

title: Wikijunior:Human Body/Stub Template


text:
Bartending/Cocktails/Bob Dylan

The Bob Dylan is a simple blended drink.

Ingredients

 * 12oz Surge
 * 4oz Jägermeister
 * 16oz Ice

Glass

 * Tall Glass

Procedure

 * 1) Blend ingredients in blender until smooth.

Related cocktails

 * Mountain Meister

title: Bartending/Cocktails/Bob Dylan


text:
Bartending/Cocktails/B-50 series

The B-50 series is a series of layered shots including:

 * B-51
 * B-52
 * B-52 with Bombay Doors
 * B-53
 * B-54
 * B-57

title: Bartending/Cocktails/B-50 series


text:
Category:Flaming beverages

Flaming cockroach: Served at Mexican restaurants. It is a shot of tequila topped with Bacardi 151, which is lit on fire.

Hazard
Flaming beverages are an obvious fire hazard and should not be attempted by the inexperienced. There have been several cases of injuries from flaming beverages. Always extinguish the flames completely before drinking. Disfiguring second degree burns have been reported on inexperienced drinkers.

title: Category:Flaming beverages


text:
User talk:Nourishment

Hello, and welcome to Wikibooks!

Here are some tips to help you get started:
 * To learn the wiki-markup-language syntax, see Help:Editing.
 * You should sign your name on Talk and vote pages using four tildes, like this: ~~~~
 * There is a box at the top of the edit window that will insert this, too; it looks like part of a signature.
 * Remember to conduct any editing experiments in the sandbox.
 * You can tell the community something about yourself in your userpage.
 * You can get to this page by clicking the tab at the top of the page labeled with your registered username.
 * If you are a Wikipedian, see Wikibooks for Wikipedians for a primer on how things work here (it's a little different).
 * If you want to base your work here on materials from Wikipedia, please use WB:RFI (requests for importation) to bring the material over in compliance with the GFDL.
 * If you're an instructor and plan on using Wikibooks for a class project, see Guidelines for class projects
 * Please say hello at the Staff Lounge with any questions or ideas.
 * Eventually, you might want to read the Manual of Style and Policies and Guidelines.
 * Please take a look at Naming policy before starting a new book.
 * Remember to maintain a Neutral point of view.
 * Explore, be bold in editing pages, and have fun!

You will find more resources in Community Portal. If you want to ask a question, visit the Study help desk, the Staff lounge, IRC channel or ask me personally on my talk page. For site news, see the Bulletin board. It might be a good idea to add this page to your "watchlist" so that you can see when any new information is posted there. You can do that by clicking the tab labeled "watch" at the top of the page.

Good luck! -- Herby talk thyme 09:58, 2 April 2007 (UTC) Please do not add inappropriate external links to Wikibooks. Wikibooks is intended to be read without the need for external reference and requires content rather than external links particularly those which are for advertising or promotion. Inappropriate links may include (but are not limited to) links to personal web sites, links to web sites with which you are affiliated, and links that exist to attract visitors to a web site or promote a product. If you feel the link should be added to the article, then please discuss it on the article's talk page rather than re-adding it. See the welcome page to learn more about Wikibooks. Thank you. -- Herby talk thyme 09:58, 2 April 2007 (UTC)

title: User talk:Nourishment


text:
PHP and MySQL Programming/Introduction to PHP

Welcome to PHP
PHP started off as a collection of Perl scripts used to aid in the maintaining of personal home pages. Hence, it originally stood for "Personal Home Page." However, the language has grown into a huge open source initiative, used by thousands of amateur and professional programmers world wide. It now is officially known as "PHP: Hypertext Preprocessor," which is a recursive acronym. (For some strange reason, open source programmers seem to love recursive acronyms...)

The reason it is known as a preprocessor and not merely as a processor, is due to the fact that the php files are sent by the webserver to the PHP preprocessor to be processed. the resulting HTML (Hyper Text Markup Language), is then sent across the internet to the web browser requesting the php page.

PHP has traditionally been used for adding dynamic content onto previously static webpages; however, due to the rapid development of the language, it is now used for writing command line tools, and now has GTK bindings allowing the programmer to write GUI applications!

Since the beginning of version 5 of PHP, with the inclusion of Zend Engine II as PHP's foundation, PHP now can be used to write Object Oriented applications.

You can download PHP free of charge (as it/is an Open Source programming language) from http://www.php.net


text:
Talk:PHP and MySQL Programming

I think there are some replicated pages in this book. Some pages are like this: Programming:PHP and MySQL:Introduction and other like this Programming:PHP and MySQL/File Handling

Worst, the inter-page links are also confused causing some page to be replicated. I'll try to look into this and try to resolve the page into using the second type of links, and subpaging. I Hope there is no outside link that points to the deleted page. -- The Kid 10:20, 2 April 2007 (UTC)

OK, finished most of everything. I've moved the pages. Note: due to my mistake, I forgot to use the move feature, instead copying them one-by-one. Only the last page is moved properly by the move feature. And when I tried to move the other pages again, with the proper move feature, they can't be moved because there is an article of the same name. Strangely enough, the first and second section's page content went missing. I'll tag the "soon should be deleted" pages with the delete tag, including the missing first and second one. -- The Kid 12:34, 2 April 2007 (UTC)

 * Instead of outright deleting the duplicate pages, I merged them together to fix the problem and now the old pages redirect to the new names too. I'm going to go ahead and make a few other improvements that I can see, while I got my eye on the book. --dark [[Image:Yin yang.svg|12px]] lama 13:53, 2 April 2007 (UTC)

title: Talk:PHP and MySQL Programming


text:
PHP and MySQL Programming/Syntax Overview

 * Enclose PHP code
 * Embedded in normal HTML code
 * Within PHP tags, statements are separated by a ; (generally also followed by a new line).

Example:

//
Comments out one line

Example:

Example:

#
Same function as //

/* (text) */
Comments out everything between the /* and the */

Example:

Variables
Variables in PHP are denoted by the $ prefix.

Example:

PHP supports dynamic variables.

Example:

PHP variables do not have to be declared ahead of time, nor do they require a type definition. PHP handles all data type conversions.

 * Example:

PHP supports Boolean variables, which can be assigned either a one or a zero, or a true or false.

Example:

Helpful Definitions:

 * Equal vs Identical
 * Equal: values are equal in value, but may be of differing types. Uses == comparison operator.  E.g. false is equal to 0.
 * Identical: values are equal in value and of the same type. Uses === comparison operator.  E.g. false is identical only to false, it is not identical to 0.

Arithmetic Operators
Example:

Assignment Operators
Example:

Comparison Operators
Example:

Concatenation
Example:

Arrays
PHP supports both numerically indexed arrays as well as associative arrays.

Example:

If ... else statement
Example:

Switch statement
Example:

For statement
Example:

Foreach statement
Example:

While statement
Example:

Do ... while statement
Example:

Functions
Example:

Classes
Example:

As of PHP 5.3.3, functions with the same name as the class will no longer act as a constructor. Versions prior to 5.3.3 the  line could be replaced with   to achieve the same effect.


text:
Wikijunior talk:Human Body

Series of Questions
Could we scrap the line "Modules will focus only on answering a specific series of questions plus about the subject" from the project description? I don't feel that an appropriate set of questions could be formulated that would be usable for every module, for example, the same question could not be used for the eyes as for the blood. If the same questions were used big gaps would appear in the comprehensiveness of the modules. Urbane User  (Talk)   (Contributions)  13:28, 2 April 2007 (UTC)

 * I respect your opinion on that. What we have done in the past is change the questions somewhat to suit the topic. I think the questions help to keep consistency in the modules and give us an idea of the relative completeness of each module/article. I think that they aid the development process and help to attract new users in th early development process. Certainly I don't object to changing the text of that particular passage to something a little more open-ended. What are your thoughts? -- xixtas talk 13:43, 2 April 2007 (UTC)

 * Great start on the article on blood, BTW. Nicely written. :) -- xixtas talk 13:47, 2 April 2007 (UTC)

 * The worst thing about that sentence was that it didn't make any sense. ;) I have rephrased. If you still don't like it, use your best judgment and fix it. -- xixtas talk 02:59, 3 April 2007 (UTC)

 * Sorry i was unable to answer your previous question, i didnt get a chance to log n yesterday afternoon. Thanks for taking my suggestions on board, I think the new rephrased sentence is great. And thanks for the support on the blood article. It is very much appreciated. Urbane User   (Talk)   (Contributions)  10:11, 3 April 2007 (UTC)

Content Organization
It seems to make sense to organize this book with body systems as chapters and organs as pages under those. As an example, DigestiveSystem would be a chapter. Stomach, SmallIntestine, and LargeIntestine would be pages under that. The current pages are not named that way. Should we reorganize? If so, what is the process for doing that? Also, is there a TOC for this book? It might be easier to flesh out with that as an outline. I am happy to write that if that makes sense. Kfasimpaur 23:42, 31 May 2007 (UTC) talk

General look and original artwork
Some nice articles underway here but many of the illustrations for example from Greys anatomy anno 1918 may not seem appealing to kids. Perhaps I have a somewhat prejudice view of what kids may appreciate but I would imagine more colorful images would be popular? I wish I could make it happen but unfortunately I'm not that great at drawing...

You can still just try ... I won't judge your drawing I promise 💛 X.Smileyy (discuss • contribs) 14:56, 17 May 2018 (UTC)

Updating Development Stages
Since these haven't been updated in a while i think that while we are editing the pages we should change the development to what we think it deserves. Whether that be lowering or raising it's level. I would like to receive some feedback on what you think we should change. Thanks.

Also what do you think we should consider doing about the ears section. It seems like most of what has to be said about the ear, has been written. That said do you think we should update the development considering there is only so much we can talk about and it isn't a lot?

New Section Proposal
Hi everyone! I have a suggestion. :) I think that the reproductive system should be here. However, since this book is for children, I wanted to make sure that everyone thought that would be a good idea. If it was made, I think it would need to be separated into male and female sections. JonathanHopeThisIsUnique (discuss • contribs) 20:30, 1 September 2014 (UTC)

title: Wikijunior talk:Human Body


text: Category:Book:PHP and MySQL Programming

title: Category:Book:PHP and MySQL Programming


text:
Proteomics/Protein Separations - Centrifugation/Differential Centrifugation

Differential Centrifugation
Differential Centrifugation is a process involving multiple centrifugation steps, increasing the speed of centrifugation each time, used to separate cellular materials. This process uses a equilibrium density gradient. The mixture of cellular materials (known as homogenate) is separated into different layers based on the molecular weight, size, and shape of each type of molecules. Subsequent rounds of centrifugation will pellet first the nuclei, followed by the mitochondria, then the lysozomes, and finally the microsomes. The soluble fraction of the homogenate is what remains after these materials have been removed. To begin proteomics research focused on proteins found in one of the various differential fractions, that particular layer would first be isolated and collected and then further purification/experimentation can be carried out. A protocol for membrane protein extraction using multiple rounds of centrifugation at varying speeds can be found at http://www.westernblotting.org/protocol%20membrane%20extraction.htm.

Differential Fractions
Each fraction obtained is a partially-pure preparation from which contaminating particles can be removed by repeated washing. This is accomplished by first resuspending the pellet in an isotonic solvent and then re-pelleting using centrifugation. To purify the sample further is may then be separated using density gradient centrifugation.

Nuclear Fraction
The nuclear fraction of the homogenate can be pelleted by centrifugation at 600g for 10 minutes. This fraction will contain all material found in the nucleus including genomic DNA, proteins involved in replication and transcription, as well as other nuclear proteins and materials.

Mitochondrial Fraction
The mitochondrial fraction of the homogenate is obtained in the pellet when the post-nuclear supernatant (i.e. the supernatant of the first centrifugation ) is centrifuged at 5000g for 10 minutes. The mitochondria are sometimes called the “power house” of the cell because of their role in energy production. Mitochondria also have their own DNA unique from that which is found in the nucleus. Proteins of interest found in the mitochondria would be those involved in the conversion of organic materials into ATP through oxidative phosphorylation.

Lysosomal Fraction
The lysosomal fraction can be pelleted by centrifugation at 12,000xg for 5 minutes. Lysosomes contain important proteins for breaking down cellular waste.

Microsomal Fraction
The microsomal fraction is the pellet produced when the postmitochondrial supernatant is centrifuged at 50,000g for 60 minutes. Microsomes are small vesicles enclosed by a biological membrane. During centrifugation the endoplasmic reticulum is fragmented into microsomes.

Soluble Fraction
The soluble fraction of the homogenate is the supernatant that remains after the other materials have been pelleted out in previous rounds of centrifugation. Within this fraction soluble proteins are found. To further isolate/purify proteins found here a different method of centrifugation can be used, such as density gradient centrifugation. In fact, density gradient centrifugation can be used to further separate any of the fractions collected by differential centrifugation.

Next Chapter: Emerging and Miscellaneous Proteomics Technologies


text:
Asymptote/File IO

This section contains a discussion of the various file manipulation capabilities of Asymptote. It covers image files outputs, source code includes and data file input and output.

Image Files
Image files are created by calling the shipout function. However, this need not be explicitly included.

Source Files
Many useful modules, as discussed in the Asymptote main page, can be imported using the file import routine; for example:

 import graph.asy;

would give access to the numerous graphing functions contained in the file graph.asy.

According to the software documentation (http://asymptote.sourceforge.net), Asymptote will search for module files in the following directories (in order):
 * 1) The current directory;
 * 2) The directory .asy in the user’s home directory (%USERPROFILE%\.asy under MSDOS);
 * 3) A list of one or more directories specified by the configuration variable dir (separated by : under UNIX and ; under MSDOS);
 * 4) The Asymptote system directory (by default, /usr/local/share/asymptote under UNIX and C:\Program Files\Asymptote under MSDOS).

The working directory can be changed using the command

 string cd(string directory_string);

The return value is the new directory. If directory_string is an empty string, the system returns to the working directory at startup. Note: the option -global or -unsafe must be enabled to change the working directory.

Data Files
Data files can be input and output

title: Asymptote/File IO


text:
Proteomics/Protein Separations - Centrifugation/Density Gradient Centrifugation

Density Gradient Centrifugation
The use of density gradients has become almost routine in centrifugal fractionation of particle mixtures and purification of subcellular organelles and macromolecules. The basic idea behind the density gradient approach is that the mixture of particles to be separated is placed onto the surface of a vertical column of liquid, the density of which progressively increases from top to bottom, and then centrifuged. Although the particles in suspension are individually denser than the liquid at the top of the gradient, the average density for the sample (i.e. particles plus suspending liquid) is lower; only under such conditions could the sample zone be supported by the top of the density gradient. The two main types of density gradient centrifugation are rate-zonal separation and isopycnic separation.

Rate-Zonal Separation
In rate-zonal separation, particles are separated based on their size and mass. This means that they migrate through the gradient according to these properties - which allows their separation into distinct zones or bands, if they were layered as a thin zone onto the top of the gradient. This is useful in separating out particles with the same or very similar densities, but different sizes or masses: size is a much stronger discriminator than density in determining where particles migrate to in a given time, as sedimentation rate or velocity of a particle in a gravitational field is directly proportional to the density difference, but depends upon the square of the diameter.

Many proteins and other macromolecules, such as antibodies and virus particles, are isolated in this way.

It is generally the case that rate-zonal separations are dynamic rather than static: that is, if centrifugation is continued long enough, all the zones end up as one pellet at the bottom of the tube. It is also possible to combine rate zonal and density separations if the greatest density in the tube - for example, 1.04 to 1.23 g/cm3 for a 10 - 50% (w/v) sucrose gradient - is higher than one particular particle density, but less than the others being separated.

Isopycnic Separation
In isopycnic separation the particles migrate through the solvent gradient until they reach the point where their buoyant density is equal to that of the gradient. This is known as the isopycnic point or isodense position. Once the particles have reached their isopycnic point they will no longer move in the gradient, regardless of how much longer the centrifuge is run for. An example of this type of gradient is a caesium chloride concentration gradient. This is a salt that - for example - has a density of 1.08 g/cm3 for a 10% (w/v) solution, increasing to 1.58 g/cm3 for a 50% (w/v) solution. It and other heavy metal salts have the problems of being somewhat toxic and exerting a very strong osmotic pressure, as well as chemically affecting certain macromolecules. There are other, more inert materials better suited to isopycnic or even rate zonal separations, such as iodixanol: this is a non-ionic polymer which has very low osmolality and is capable of self-forming gradients like the heavy metal salts.

Rate vs. Isopycnic Separation: Advantages and Disadvantages
The choice of whether to try to isolate particles on rate basis or by isopycnic banding should take into account the following points:

 * For large particles such as cellular organelles, rate zonal runs are of considerably shorter duration than are isopycnic runs. This can be an important consideration where prolonged particle viability or liability are questionable.

 * Rate zonal runs are usually carried out in shallower density gradients than are isopycnic runs. Such condition can prove less damaging to particles that are osmotically active.

 * Rate zonal runs are usually carried out by using a lower RFC than is used in isopycnic runs. For certain especially fragile particles, the reduced hydrodynamic shear during sedimentation may be an aid in maintaining particle integrity.

 * The duration of centrifugation is not as critical in an isopycnic run as in a rate zonal run. To attain isopycnic banding, a certain minimum amount of centrifugation is required, but extending the centrifugation time beyond this does not much alter the results if the sample was layered on top of the gradient.

 * Generally speaking, greater numbers of particles can be separated by isopycnic density gradient centrifugation than by rate centrifugation. This is because the density gradients used for isopycnic runs are steeper and more stably support a greater quantity of sample.

Preparation of Density Gradients
Density Gradients are used not only for particle separations in the centrifuge tubes of conventional rotors, but also in special-purpose instruments such as zonal rotors, continuous flow rotors,and stay-put devices .The fundamentals of density gradient preparation are the same in nearly all the applications, but for the time being the discussion will center around gradient generation in tubes. Density Gradient may be subdivided into two main categories according to the means of preparation: step gradients and continuous gradients.

Step Gradients
Step Gradients are prepared by successively layering solutions of different density in the centrifuge tube and then layering the sample to be fractionated on top of the last "step". Step gradients are sometimes useful in density gradient centrifugation because the abrupt density steps that persist can be used as surfaces onto which particles can sediment during centrifugation. This results in discrete particle layers at each step. Special density gradient generating equipment is not required for production of step gradients. The gradient may be built up in the centrifuge tubes carefully layering one step on another, beginning with the densest step, by use of a pipette. Alternatively the gradient can be formed beginning with the least dense step by depositing each layer at the bottom of the centrifuge tube through a narrow cannula.

Continuous Gradients
Continuous density gradients are gradients in which the density changes smoothly and continuously from one limit or extreme to another. Such gradients can be produced from step gradients by allowing sufficient time for diffusion to smooth out the steps, but continuous gradients are normally prepared directly by using special devices known as gradient makers or gradient engines.

Gradient Materials
For most biological work, the ideal solute used to produce a density gradient should satisfy the following criteria:
 * The solute should be sufficiently soluble in aqueous media to produce the range of densities needed.
 * Dissolution of the solute should not result in solutions of high viscosity in the desired density range. Viscous solutions pose special mixing problems for gradient makers and are handled with some difficulty. Moreover, the sedimentation rate of a particle decreases directly in relation to the viscosity of the surrounding medium.
 * The solute should not exert too high an osmotic pressure in the desired density gradient range. The size, the shape, and the density of whole cells, membrane-enclosed subcellular organelles, and even macro molecules can be altered as these particles sediment through a density gradient if the osmotic pressure of the surrounding medium changes markedly.
 * Solutions of the gradient solute should be adjustable to the pH and ionic strengths that are compatible with the particles being separated.
 * The solute should not react with the particles being separated and should not interfere with the methods of analysis of the collected fractions.
 * Solutions of the gradient solute should exhibit a property that can conveniently be used as a measure of concentration or gradient density.
 * The solute should be readily removable from the collected gradient fractions (should that be necessary or desirable).
 * The solute should be affordable in the quantities needed.

Collecting Fractions
At the conclusion of centrifugation, the density gradient and the entangled particle zones are usually removed from the tube (or rotor) and collected as a series of fractions. This may be achieved in several ways. One of the oldest and simplest methods is to puncture the bottom of each centrifuge tube and allow the contents to slowly drip out. The gradient may also be removed by carefully lowering a narrow cannula to the bottom of the tube and withdrawing the gradient by use of a peristaltic pump. In both procedures the gradient exits the tube dense end first, and thus the separated particles are collected in order of decreasing sedimention rate or density. A third option is to puncture the tube at the location in the gradient of the material of interest and extract it manually. For a detailed description of this see the protocol at http://people.rit.edu/rhrsbi/GEPages/LabManualPDF5ed/23%20Plasmid%20Prep.pdf. The diagram below demonstrates this process in the collection of the plasmid DNA fraction; however, one can see how easily this could be applied to the protein fraction instead.

Measuring Gradient Density
Since the density of a solution is its mass:volume ratio, measurement of these two parameters in successive aliquots of the collected gradient reveals the gradient's profile. However this approach is awkward and time consuming and is rarely used in connection with density gradient centrifugation. Instead, the refractive index of small drops of liquid taken from different regions of the gradient is determined, and the corresponding densities obtained from tables or curves relating refractive index to density.

Light Refraction and Snell's Law
The speed of the light changes as light passes from one medium into another. If the light passes across the interface between the two media at any angle other than 90 degree, the direction of the light is also changed. The refractive index of a substance is a measure of its ability to bend the light and is related to the substance's density. For more detailed information on this subject see Snell's law at Wikipedia.

Next Section: Differential Centrifugation


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Talk:Asymptote/File IO

This page needs lots of work, of course. I just wanted to have a coherent reference for data file input and output. Run4flat 16:01, 2 April 2007 (UTC)

yes, please, can anyone put an example on how to read a file with triplets of numbers and convert them to a path3?

title: Talk:Asymptote/File IO


text: User talk:64.251.50.68

title: User talk:64.251.50.68


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User talk:66.37.63.162

Thanks for experimenting with Wikibooks. Your test worked, and has now been removed. Please use Sandbox for any other tests you want to do, since testing material in modules will normally be removed quickly. Please see the welcome page if you would like to learn more about contributing to our project. Thanks. -- Herby talk thyme 17:28, 2 April 2007 (UTC)

title: User talk:66.37.63.162


text: Dutch/Vocabulary/Colours

title: Dutch/Vocabulary/Colours


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Hacking/Tools/Network/Nessus/OpenVAS

OpenVAS evolved from Nessus when Tenable put Nessus under a restrictive license. Tenable had some trouble with people rebranding Nessus as their own product, and unfortunately had to make this move. As a result, OpenVAS appeared.

OpenVAS resides at http://www.openvas.org/; the project suffered an infrastructure problem as soon as it opened, but the mailing lists show healthy development activity and the project may very well take off.

title: Hacking/Tools/Network/Nessus/OpenVAS


text:
Dutch/Vocabulary/Fruit

Memorize these fruits. Push on the button to hear the pronunciation

You can also use Quizlet (32 terms)

For a self-test see: Dutch/Vocabulary/Fruit/Selftest

title: Dutch/Vocabulary/Fruit


text:
Hacking/Tools

General tools

 * , are operating systems for penetration testing.
 * — provides information about security vulnerabilities and aids in penetration testing and IDS signature development
 * Metasploit Unleashed – Free Ethical Hacking Course
 * — GUI for Metasploit
 * Veil generates Metasploit payloads that bypass common anti-virus solutions
 * is a proprietary vulnerability scanner.
 * NASL — The — a scripting language that is used by vulnerability scanners like Nessus and OpenVAS.
 * https://beefproject.com/ The Browser Exploitation Framework.
 * Burp Suite
 * https://NoDistribute.com/ — privately scans files online with multiple different anti-viruses
 * for open-source intelligence and forensics
 * — advanced search
 * — search engine for the Internet of Everything

Network tools

 * nmap discovers hosts and services on a computer network by sending packets and analyzing the responses.
 * displays route and measures transit delays of packets across an IP network.
 * — a network administration command-line tool for querying the Domain Name System (DNS)
 * queries the to obtain the mapping between  and, or other s.
 * — collection of userspace utilities for controlling and monitoring various aspects of networking in the Linux kernel, including routing, network interfaces, tunnels, traffic control, and network-related device drivers
 * netdiscover — arp based network address discovering tool
 * is a packet sniffer/network traffic monitoring tool.
 * is a free Linux network analyzer and networking toolkit.
 * is a free and open source network security tool for MITM attacks on LAN.
 * Xerosploit — MITM framework. Powered by bettercap and nmap.
 * cloudflare-scrape to bypass Cloudflare's anti-bot page
 * — set of password sniffing and network traffic analysis tools
 * BDFProxy — BackdoorFactory + mitmProxy
 * https://www.robtex.com/
 * — open-source web application security scanner
 * — open-source web application security scanner

General purpose tools
 * s: ,
 * — packet filter rules configuration

Defense
 * http://www.XArp.net — advanced ARP spoofing detection

Wi-Fi tools

 * https://github.com/ZerBea/hcxtools converts Wi-Fi dump files to hashcat formats
 * https://github.com/brannondorsey/wifi-cracking cracks WPA/WPA2 Wi-Fi Routers with Airodump-ng and Aircrack-ng/Hashcat

 * https://sourceforge.net/projects/crunch-wordlist/ - wordlist generator
 * https://sourceforge.net/projects/crunch-wordlist/ - wordlist generator
 * https://sourceforge.net/projects/crunch-wordlist/ - wordlist generator
 * https://sourceforge.net/projects/crunch-wordlist/ - wordlist generator
 * https://sourceforge.net/projects/crunch-wordlist/ - wordlist generator

Other

 * https://github.com/laramies/theHarvester — E-mails, subdomains and names Harvester - OSINT
 * dirb — Web Content Scanner
 * https://sqlmap.org/ — detecting and exploiting
 * https://app.any.run/ — interactive online malware analysis service

Targets

 * https://www.vulnhub.com/
 * https://www.root-me.org/?lang=en
 * http://www.vulnweb.com/
 * https://dvwa.co.uk/ - Damn Vulnerable Web Application
 * https://github.com/rapid7/metasploitable3 - target for testing exploits with Metasploit
 * https://developer.microsoft.com/en-us/microsoft-edge/tools/vms/

Further reading
 * https://sectools.org/
 * Decoding Obfuscated JavaScript Using Google Chrome.
 * https://github.com/topics/security
 * https://outpost24.com/blog/wps-cracking-with-reaver
 * https://kalilinuxtutorials.com/mdk3/
 * 25 Best Ethical Hacking Tools & Software for Hackers (2021)
 * https://medium.com/hacker-toolbelt
 * 25 Best Ethical Hacking Tools & Software for Hackers (2021)
 * https://medium.com/hacker-toolbelt

title: Hacking/Tools


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User talk:170.158.132.51

Please stop adding nonsense to Wikibooks. It is considered vandalism. If you would like to experiment, use the sandbox. Thank you. -- Jim Thomas (aka Jomegat) 18:25, 2 April 2007 (UTC)

title: User talk:170.158.132.51


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Hacking/Tools/Network

/Changing Your MAC Address

title: Hacking/Tools/Network


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User talk:70.18.93.121

You are blocked - please contribute properly when the block ends -- Jim Thomas (aka Jomegat) 19:14, 2 April 2007 (UTC)

title: User talk:70.18.93.121


text:
Dutch/Lesson Afrikaans

Welkom by die Afrikaans les

 * Daar is 'n eie wikiboek vir Afrikaans, hierdie is net 'n vergelyking van die twee tale.
 * Er is een eigen wikiboek voor Afrikaans, dit is slechts een vergelijking van de twee talen.
 * Afrikaans has its own wikibook. This page discusses the relationship between the two sister languages.

Afrikaans & Nederlands
Dutch is used in the countries The Netherlands, Belgium, Suriname, Netherlands Antilles & Aruba, sometimes in Indonesia and some neighbouring parts of Germany and France. But if you speak Standard Dutch you can also hold conversations very easily in Southern Africa, in South Africa and Namibia.

Since the founding of Kaapstad (Cape Town) in 1652 a variety of Dutch was spoken at the Cape, gradually spreading over much of Southern Africa. Since 1806 the political ties were severed and the spoken languages evolved in their own directions, much as English did in the U.S. and French did in Quebec. Some Dutch dialects and Afrikaans are still very close to each other and the differences between Dutch dialects are at least as big as between Dutch and Afrikaans. In fact, until 1925 there was only one written standard legally recognized both in South Africa and in Belgium and the Netherlands and Dutch had been the official language of both Boer Republics.

Unfortunately, this written standard was rather artificial and archaic and did not reflect what people actually spoke. For example the standard still had case endings and three genders (masculine, feminine and neuter). Only certain dialects of Flanders and the southern part of the Netherlands still had at least three genders in the spoken language. The northern Netherlands only had two genders and South Africa only one. The inflectional system was already gradually becoming disused in the Middle Ages and basically collapsed in the 16th century in spoken Dutch, but later grammarians decided that it had to be preserved— even brought back— at all costs. On top of that the spoken language of South Africa had a much simplified verbal system, e.g. it no longer used the simple past tense. There were also numerous differences in pronunciation and semantics.

The discrepancies between the single written standard and what people actually spoke were so large that they created serious educational problems and formed an impediment to social progress both in Africa and in Europe.

This was why the Kollewijn spelling (1891) proposed radical changes for the spelling of the language. It is also known as "Schrijf zoals je praat / Skryf hoe jy praat-spelling" (Write-as-you-talk spelling). In South Africa, where the discrepancies were the most conspicuous, his ideas were implemented in the 1920's with considerable vigor.

In the Netherlands and Belgium (and their colonies) his ideas were dismissed as outrageous and iconoclastic. It was also feared that what had been one language would splinter into many, each of which would be unable to compete in the modern world.

In 1925 Afrikaans was officially recognized as a separate language with its own spelling and grammar, much closer to what people actually spoke. In Europe it was only after the Second World War that the educational and political establishment finally threw in the towel and followed the Afrikaans example. In 1947 the spelling was revised in such a way that case endings (notably the -n in the masculine singular accusative: den) were made optional. Rapidly it disappeared from use. Many silent and superfluous letters were omitted, e.g.:

 * de menschen wenschen → die mense wens
 * de boeken van dien aardigen kleinen jongen → die boeke van die aardige klein jong

The reform of 1947 was not quite as sweeping as the one in 1925.

For example the word for at home is still written as thuis (from: te huis) in Dutch, but as tuis in Afrikaans. Similarly, thans (from te hands: now) is written as it is pronounced in Afrikaans: tans.

In part the reluctance to reform had to do with the fact that earlier ideas in Flanders to create a separate standard closer to what was spoken there had largely been abandoned. In Belgium the language was under considerable pressure from a French speaking elite and could ill afford further fragmentation. Even within Flanders the dialects were by no means homogeneous with West-Flemish in the west, Brabantian in the middle and Limburgian in the east showing considerable differences. There was clearly a desire to keep the written umbrella unified despite this considerable variety in the spoken language. This led to increased linguistic cooperation between Flanders and the Netherlands, a more or less wholesale adoption of the northern standard language as umbrella and the creation of the Taalunie. From the 1960s on the Dutch speaking majority in Belgium has largely achieved its emancipation and there is a bit more interest in the idiosyncrasies of the southern varieties of Dutch.

The ties with South Africa in the mean time had become all but severed because the Apartheid government there - amongst other things - emphasized the uniqueness of the Afrikaans language. In fact in 1961 all linguistic ties were broken, when Dutch ceased to be one of the official languages of the new Republic of South Africa. The Netherlands and Belgium increasingly joined the boycott against apartheid. Since 1994 there is a slow process of renewal of ties but the languages have continued to evolve in different directions in the meantime.

Inleiding
Afrikaans: Afrikaans is een van die elf amptelike tale in Suid-Afrika en is ook die grootste, maar nie amptelike taal nie van Namibië. Afrikaans, 'n betwiste kreool van Nederlands, word gepraat deur 6 miljoen mense in Suid-Afrika as huistaal. Naas die 6 miljoen is daar ook 10 miljoen wat Afrikaans praat as tweede taal, vaak naas Engels, Xhosa of Zoeloe

 * Let op: Hierdie mense wat Afrikaans praat is nie alleenlik blanke Suid-Afrikaners van Nederlandse afkoms nie maar word ook gepraat deur die sogenaamde kleurlinge en swart Suid-Afrikaners.

Tot 1925 het Afrikaans as Nederlands gereken, maar in 1961 het Afrikaans Nederlands offisieel vervang. Tot dié tyd het die mense Afrikaans en Nederlands beskou as sinonieme. Na 1961 heet die taal Afrikaans. Nederlands is oorspronklik die taal van die Nederlandse koloniste, toe die Boere en nou die Afrikaners. Deesdae word die taal deur mense van alle kleure gepraat. Die taal is die meest verspreide taal in Suidelike Afrika en meer as 60% van die Namibiërs kan 'n proffesionele gesprek in Afrikaans voer.

Introduction
English: Afrikaans is one of the eleven official languages in South Africa and also the biggest, but not an official language of Namibia. Afrikaans, a creole of Dutch, is spoken by 6 million people in South Africa as a mother tongue. Beside those 6 million there are also 10 million people that speak Afrikaans as a secondary language, often next to English, Xhosa or Zulu.

 * Note: This is not only the white South Africans of Dutch descent but also the "coloureds" and also many black South Africans.

It was in 1925 that Afrikaans was recognized as Dutch in South Africa, but in 1961 Afrikaans replaced Dutch officially, till those times it was considered as synonyms. After 1961 the language is called Afrikaans. Dutch was originally the language of the Dutch colonists, later Boers and now Afrikaners. But these days the language is used by people of all colours. The language is the most spread out language in Southern Africa and more than 60% of the Namibians can have a professional conversation in Afrikaans.

Orthographic differences
Dutch uses the digraph ij for words with a /ɛɪ̯/ diphthong that historically had a long /i:/ sound and still do in many dialects. Afrikaans has opted to use y in its spelling.

Dutch has two ways to spell the same diphthong au and ou. Etymologically they are different, but not in pronunciation anymore. Afrikaans has opted to only use ou.

Phonetic differences
Dutch has voiced consonants like z, v and g that are not pronounced voiced by all speakers or in all positions. There also also unvoiced counterparts written as s, f and ch. In Afrikaans they are all unvoiced and z and ch have been dropped from the orthography.

 * English: sea
 * Afrikaans: see
 * Dutch: zee

Intervocalic -g- has mostly been lost in Afrikaans:

 * English: rain
 * Afrikaans: reen
 * Dutch: regen

Some final consonant clusters have been simplified in Afrikaans

 * English: night
 * Afrikaans: nag
 * Dutch: nacht

However, in the plural the lost t may reappear:

 * English: nights
 * Afrikaans: nagte
 * Dutch: nachten

Verbs
One major difference between the two languages is that Dutch retains the simple past tense, Afrikaans does not:

 * I learn - I learned - I have learned
 * ik leer - ik leerde - ik heb geleerd
 * ek leer - ek het geleer

This means that the use of the tenses is different in Afrikaans compared to Dutch.

In the present tense Dutch typically has three forms:

 * ik leer
 * jij, hij leert
 * wij, jullie, zij leren

In Afrikaans there is only one: leer

Verb position
Afrikaans has retained much of the West-Germanic word order that often is the cause of Anglophone frustration when learning Dutch, although there are also differences with Dutch word order.

Negation
In Dutch negation is often done by simply adding the word niet (not) to the sentence. Afrikaans has double negation, adding the word nie twice

 * English: I have seen him - I have not seen him
 * Dutch: Ik heb hem gezien - Ik heb hem niet gezien
 * Afrikaans: Ek het hom gesien - Ek het hom nie gesien nie.

Gender
In Dutch there are nouns that take the definite artikel de and those that take het (neuter gender). In Afrikaans all nouns have the same gender as in English:

 * English: the day   -  the house
 * Afrikaans: die dag - die huis
 * Dutch:  de dag -  het huis

Dutch gender has consequences for e.g. the inflections that the adjectives take. Consequently, Afrikaans grammar is different on this point.

Plurals
Dutch has two major ways of forming the plural -en and -s. The final -n of the former is not always pronounced depending on region, how quickly one speaks, whether the next word starts with a vowel etc. In Afrikaans it was no longer pronounced at all and was therefore dropped in the spelling.

 * Dutch: het huis  - de huizen
 * Afrikaans: die huis - die huise

Sometimes where Dutch has -en Afrikaans will have -s, e.g. verbal nouns ending in -ing

 * Dutch: verwachting - verwachtingen
 * Afrikaans: verwagting - verwagtings

Vocabulary
Dutch has many words that were borrowed from French in the 18th, 19th even 20th centuries that have not always reached Afrikaans. An example is the word douche. It is of French origin and in Dutch it means shower. In Afrikaans the word for shower is stortbad or stort. In Dutch this word is comprehensible but odd and archaic.

Both languages have a lot of borrowings from English, but for Dutch that is relatively new phenomenon. Afrikaans has resisted the intrusion far more deliberately than Dutch has. It often resorts to calques or translation borrowing where Dutch either has its own indigenous expression of simply uses the English word.

Afrikaans has also picked up more words from Indonesian, particularly the variety of Afrikaans known as Slaams, spoken by the Islamic minority of the Cape who are mostly of Malay descent.

Afrikaans evolved many terms to describe nature in all of its rich South African variety. Sometimes the same word is used for a different animal in the two languages,e.g. the word eland:

title: Dutch/Lesson Afrikaans