Wogking Of Agp Computer Science Essay

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Is called the Accelerated Graphics Port. Accelerated Graphics Port A high-speed 32-bit port from Intel for attaching a display adapter to a PC. It provides a direct connection between the card and memory, and only one AGP slot is on the motherboard. AGP was introduced as a higher-speed alternative to PCI display adapters, and it freed a PCI slot for another peripheral device. The brown AGP slot is slightly shorter than the white PCI slot and is located about an inch farther back. AGP was superseded by PCI Express.

The original AGP standard (AGP 1x) provided a data transfer rate of 264 Mbytes/sec. AGP 2x is 528 Mbytes/sec. AGP 4x is 1 Gbyte/sec. AGP 8x is 2 Gbytes/sec. See AIMM, PCI Express, PC data buses and motherboard.

AGP 8x is 2 Gbytes/sec. See AIMM, PCI Express, PC data buses and motherboard.

Accelerated Graphics Port: an Intel-designed 32-bit PC bus architecture introduced in 1997 allowing graphics cards direct access to the system bus (currently up to 100MHz), rather than going through the slower 33MHz PCI bus. AGP uses a combination of frame buffer memory local to the graphics controller, as well as system memory, for graphics data storage, vastly increasing the amount of memory available for 3D textures.

The current PCI bus supports a data transfer rate up to 132 MB/s, while AGP (at 66MHz) supports up to 533 MB/s! AGP attains this high transfer rate due to its ability to transfer data on both the rising and falling edges of the 66MHz clock, and through new design advances that have made data transfer modes more efficient. Direct Memory Execute (also known as DIME) is probably the most important feature of AGP. AGP graphic chips have the capability to access main memory directly for the complex operation of texture mapping. AGP provides the graphics card with two methods of directly accessing texture maps in system memory: pipelining and sideband addressing. In pipelining, AGP makes multiple requests for data during a bus or memory access. PCI makes one request, and does not make another until the data it requested has been transferred.

AGP standards are currently set as the main type of graphics cards for all computers. Find out where to find the AGP standards and get prices for AGP.. AGP and AGP graphics cards are now the standard for processing graphics on computers. Like all hardware, the technology and specifications...

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AGP Memory Improvements

From  How AGP Works

AGP memory is RAM that is designated for use by the graphics card on the fly. Learn about AGP memory and how AGP saves memory through the use.. AGP improves the process of storing texture maps by allowing the operating system to designate RAM for use by the graphics card on the fly...

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Introduction to How AGP Works

The AGP enables your computer to have a dedicated way to communicate with the graphics card, which enhances the look of graphics. Find out how AGP..Computer Hardware Image Gallery The AGP enables your computer to have a dedicated way to communicate with the graphics card, which enhances the look...

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AGP Graphics Rendering

From  How AGP Works

AGP graphics rendering happens faster because of pipelining, a dedicated port and sideband addressing. Find out other ways AGP graphics rendering.. AGP is built on the idea of improving the ways that PCI transports data to the CPU. Intel achieved this by addressing all of the areas where PCI...

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Get Off the PCI Bus

From  How AGP Works

The PCI bus design is what the AGP is based on, however the AGP has a dedicated connection to the CPU. Learn about the Peripheral Component.. In 1996, Intel introduced AGP as a more efficient way to deliver the streaming video and real-time-rendered 3-D graphics that were becoming more...

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PCI Graphics Rendering: Wasting RAM

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Speed is not the only area where AGP has bested its predecessor. It also streamlines the process of rendering graphics by using system memory more...

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Introduction to How PCI Express Works

The AGP... performance, and can replace the AGP slot. Photo courtesy Consumer Guide Products Thank You Thanks to Joshua Senecal for his assistance...

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Plug and Play

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PCI Express and Advanced Graphics

From How PCI Express Works

PCIe can eliminate the need for the AGP by accepting more data and supplying more power to video cards. Learn how PCIe will change the future.. We've established that PCIe can eliminate the need for an AGP connection. A x16 PCIe slot can accommodate far more data per second than...

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PCI Connection

From How Graphics Cards Work

Through one of three interfaces: Peripheral component interconnect (PCI) Advanced graphics port (AGP) PCI Express (PCIe) PCI Express is the newest...

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Inside the AGP

Get Off the PCI Bus

In 1996, Intel introduced AGP as a more efficient way to deliver the streaming video and real-time-rendered 3-D graphics that were becoming more prevalent in all aspects of computing. Previously, the standard method of delivery was the Peripheral Component Interconnect (PCI) bus. The PCI bus is a path used to deliver information from the graphics card to the central processing unit (CPU). A bus allows multiple packets of information from different sources to travel down one path simultaneously. Information from the graphics card travels through the bus along with any other information that is coming from a device connected to the PCI. When all the information arrives at the CPU, it has to wait in line to get time with the CPU.

Photo courtesy

PCI slots on a motherboard

This system worked well for many years, but eventually the PCI bus became a little long in the tooth. The Internet and most software were more and more graphically oriented, and the demands of the graphics card needed priority over all other PCI devices.

Typical example of an AGP-based graphics card

AGP File Specification

Introduction

File Format

Describing Breaks and Continuity

Describing Scaffolds with Unknown Orientation

Validation

Examples

Introduction:

What it is: Describes the assembly of an object. This object can be a contig, a scaffold (supercontig), or a chromosome. Each line (row) of the AGP file describes a different piece of the object, and has the column entries defined below. Extended comments follow. The format was initially developed during the early assembly phase of the human genome by UCSC, EBI and NCBI. Special thanks to UCSC for their nice web site (where I was able to obtain additional information).

What it is not: a description of the alignments between components used to construct the larger molecule. Not all of the information in proprietary assembly files can be represented in the AGP format. It is also not for recording the spans of features like repeats or genes.

Definitions:

Contig:

a non-redundant sequence formed by joining, based on sequence overlap, one or more smaller sequences. The smaller sequences can be individual sequence reads (commonly called traces) or entire clone sequences. There should be no gaps in a contig (although there may be short runs of Ns due to ambiguous base calls).

Scaffold (supercontig):

a non-redundant sequence formed by joining one or more contig sequences. The distinction is that no sequence overlap is required to construct the larger sequence. Additional information, such as clone end analysis, can support the relationship. There can be, and typically there are, gaps in a scaffold.

Gap:

a sub region within an object where there is no known sequence. Generally represented as a series of the letter 'N'

Component:

a sequence used to construct a larger sequence.

File Format:

One feature of the AGP file is that column definitions change depending on whether the line is a component line or a gap line. There is a single column definition up to column 5, then each column will have two definitions,dependingon the value in column 5.

AGP File Format

column

content

description

1

object

This is the identifier for the object being assembled. This can be a chromosome, scaffold or contig. If the object is a chromosome and an accession.version identifier is not used to describe the object, then the naming convention is to precede the chromosome number with "chr" (if a chromosome) or "LG" (if a linkage group). For example: chr1. If the object is a contig or scaffold, then the identifier needs to be unique within the assembly.

2

object_beg

The starting coordinates of the component/gap on the object in column 1. These are the location in the object's coordinate system, not the component's.

3

object_end

The ending coordinates of the component/gap on the object in column 1. These are the location in the object's coordinate system, not the component's.

4

part_number

The line count for the components/gaps that make up the object described in column 1.

5

component_type

The sequencing status of the component. These typically correspond to keywords in the International Sequence Database (GenBank/EMBL/DDBJ) submission. Current acceptable values are:

A

Active Finishing

D

Draft HTG (often phase1 and phase2 are called Draft, whether or not they have the draft keyword).

F

Finished HTG (phase 3)

G

Whole Genome Finishing

N

gap with specified size

O

Other sequence (typically means no HTG keyword)

P

Pre Draft

U

gap of unknown size, typically defaulting to predefined values.

W

WGS contig

6a

component_id

If column 5 not equal to N: This is a unique identifier for the sequence component contributing to the object described in column 1. Ideally this will be a valid accession.version identifier assigned by GenBank/EMBL/DDBJ. If the sequence has not been submitted to a public repository yet, a local identifier should be used.

6b

gap_length

If column 5 equal to N: This column represents the length of the gap.

7a

component_beg

If column 5 not equal to N: This column specifies the beginning of the part of the component sequence that contributes to the object in column 1 (in component coordinates).

7b

gap_type

If column 5 equal to N: This column specifies the gap type. The combination of gap type and linkage (column 8b) indicates whether the gap is captured or uncaptured. In some cases, the gap types are assigned a biological value (e.g. centromere).

Accepted values:

fragment:

gap between two sequence contigs (also called a 'sequence gap').

clone:

a gap between two clones that do not overlap.

contig:

a gap between clone contigs (also called a "layout gap").

centromere:

a gap inserted for the centromere.

short_arm:

a gap inserted at the start of an acrocentric chromosome.

heterochromatin:

a gap inserted for an especially large region of heterochromatic sequence (may also include the centromere).

telomere:

a gap inserted for the telomere.

repeat:

an unresolvable repeat.

8a

component_end

If column 5 not equal to N: This column specifies the end of the part of the component that contributes to the object in column 1 (in component coordinates).

8b

linkage

If column 5 equal to N: This column indicates if there is evidence of linkage between the adjacent lines.

Values:

yes

no

9a

orientation

If column 5 not equal to N: This column specifies the orientation of the component relative to the object in column 1.

Values:

+

plus

-

minus

0 (zero)

unknown

na

irrelevant

By default, components with unknown orientation (0 or na) are treated as if they had + orientation.

9b

 

If column 5 equal to N: This column is empty- there is no filler. A tab should be inserted after the 8 th column though so that all lines have 9 columns.

Extended comments:

Columns should be tab delimited. Lines end with a new line (\n). There should be no extra space around the individual tokens.

All coordinates given in the file are 1-based inclusive (not 0-based). i.e. the first base of an object is 1 (not 0).

Evidence of linkage. In general, evidence of linkage is provided by end pairs (sometimes referred to as mate pairs). Although, other evidence could be used such as transcript alignments). In some cases, evidence of linkage may be indirect. For example, given the following scaffold:

     A--B--C--D

Where A, B, C and D are components, there could be end pairs linking A and B and end pairs linking A and C. There might be no pairs linking B and C but their linkage is implied.

If the object is a contig or scaffold, the object should not start with a gap line. A chromosome will frequently start or end with one or more biological gap types (e.g. telomere or short_arm).

A gap of type fragment will usually be flanked by components and not by other gap lines. Typically, successive gap lines are not encouraged, except in the case of gaps implying some biologically defined entity (such as centromere, heterochromatin, etc.).

Coordinates of the object are all with respect to the plus strand, no matter the orientation of the component.

object_beg (column 2) should always be less than or equal to object_end (column 3).

component_beg (column 7) should always be less than or equal to component_end (column 8).

Each object must start with a part_num of 1 (column 4) and an object_beg coordinate of 1 (column 2).

Gap lengths must be positive. Negative gaps and gap lines with zero length are not valid.

For negative gaps or gaps of unknown size, use 100 as the gaps size, as that is the GenBank/EMBL/DDBJ standard for gaps of unknown size.

In the case of an GenBank/EMBL/DDBJ submission, the object identifier should be unique not only within the assembly but also across different versions of the assembly. For example, chrUn01.0001 in the first version of a genome and chrUn02.0001 in the second version.

Any text after a # symbol is assumed to be a comment

The use of comment lines at the head of the file is encouraged. Useful information to include in such headers is:

organism name

assembly name

a description of any non-standard object identifiers

Describing breaks and continuity:

Information about continuity is provided by a combination of the values in 7b and 8b that provide information on building the object. This first version of this specification did not specifically define how to use these columns, thus there has been a divergence in how they are currently used. Below is a proposal on how information should be encoded.

column 7b

column 8b

Interpretation and description

contig

no

Break scaffold

A contig gap suggests a break between adjacent scaffolds implying no linkage.

contig

yes

Invalid

clone

no

Break scaffold

There may be a clone slated for the gap, but there is no evidence of linkage suggesting how this clone relates to its neighbors.

clone

yes

Do not break scaffold

There is evidence linking a clone to sequence on both sides of the gap. Default size is 50000 (entered in column 6b)

fragment

no

Do not break scaffold

A fragment gap implies that there is clone coverage across the gap, and therefore implies linkage. The 'no' in 8b suggests the adjacent sequences have unknown order or orientation. For example, gaps between sequence contigs in an HTGS_PHASE1 BAC clone will typically be 'fragment no' type gaps. Default gap size is 100 (entered in column in 6b).

fragment

yes

Do not break scaffold

Same as above, although the' yes' here suggests the adjacent sequences have known order and orientation. Gaps between sequence contigs that are linked by mate-pair evidence will typically be 'fragment yes' type gaps. For example, gaps between sequence contigs in scaffolds from a WGS assembly.

repeat

no

Break scaffold

If an unresolvable repeat unit is not spanned by clones, the linkage will be 'no'.

centromere/ short_arm/ heterochromatin/telomere

no

Break scaffold

centromere/ short_arm/ heterochromatin/telomere

yes

Invalid

Describing scaffolds with unknown orientation:

Scaffolds can sometimes be positioned along a chromosome or linkage group without there being sufficient data to orient the scaffold. Such placed but unoriented scaffolds can be indicated in an AGP that specifies how a chromosome or linkage group is assembled from scaffolds by using '0' in the orientation column (9a) (see the example "chromosome from scaffolds"). It is not appropriate to use an orientation of '0' in an AGP that specifies how a chromosome is assembled from contigs, except for any contigs that are not scaffolded to other components (singletons). Using an orientation of '0' for all the contigs in a multi-component scaffold is misleading because to do so implies that the contig lies at the position indicated but could be in either orientation. Depending on the orientation of the scaffold, however, the contigs in an unorientated multi-component scaffold either lie at the indicated position in the '+' orientation (the default) or at a different position in the '-' orientation. The preferred method to indicate that scaffolds have been placed but their orientation is unknown is to provide a chromosome-from-scaffold AGP. Alternatively, a separate file listing placed but unoriented scaffolds can be provided to supplement a chromosome-from-contig AGP that uses the default orientation of '+' for the component contigs in unoriented scaffolds.

Validation:

File structure needs to be validated in the following ways:

Columns are tab delimited

All columns of numeric data must contain positive integers

Accession identifiers (and versions) must be valid

Columns with controlled values must only use those values

All columns must have some data (except 9b)

File content needs to be validated in the following ways:

Each object must start with a part_num of 1 and an object_beg coordinate of 1.

All object ranges should be sequential and non-overlapping

object_beg must be less than or equal to object_end

component_beg must be less than or equal to component_end

The span specific for a component must be valid.

The length of the span specified for the component (in columns 7 and 8) must match the length of the span specified for the object (in columns 2 and 3).

If no gap lines exist between components, the defined switch points should be consistent with an alignment of the two components.

All gap lengths must be 1 base or longer.

Examples:

Scaffold from contig (WGS)

Chromosome from scaffold (WGS)

Chromosome from contig (WGS)

Chromosome from contig (BAC)

AGP Memory Improvements

AGP improves the process of storing texture maps by allowing the operating system to designate RAM for use by the graphics card on the fly. This type of memory is called AGP memory or non-local video memory. Using the much more abundant and faster RAM used by the operating system to store texture maps reduces the number of maps that have to be stored on the graphics card's memory. In addition, the size of the texture map your computer is capable of processing is no longer limited to the amount of RAM on the graphics card.

The other way AGP saves RAM is by only storing texture maps once. It does this with a little trickery. This trickery takes the form of a chipset called the Graphics Address Remapping Table (GART). GART takes the portion of the system memory that the AGP borrows to store texture maps for the graphics card and re-addresses it. The new address provided by GART makes the CPU think that the texture map is being stored in the card's frame buffer. GART may be putting bits and pieces of the map all over the system RAM; but when the CPU needs it, as far as it's concerned the texture map is right where it should be.

Advantages of AGP

Memory:-

Another issue has been the increasing demands for video memory. As 3D computing becomes more mainstream, much larger amounts of memory become required, not just for the screen image but also for doing the 3D calculations. This traditionally has meant putting more memory on the video card for doing this work.

Faster:-

The idea behind AGP is simple: create a faster, dedicated interface between the video chipset and the system processor. The interface is only between these two devices; this has three major advantages: it makes it easier to implement the port, makes it easier to increase AGP in speed, and makes it possible to put enhancements into the design that are specific to video.

Not -expandible:-

AGP is considered a port, and not a bus, because it only involves two devices (the processor and video card) and is not expandable.

One of the great advantages of AGP is that it isolates the video subsystem from the rest of the PC so there isn't nearly as much contention over I/O bandwidth as there is with PCI. With the video card removed from the PCI bus, other PCI devices will also benefit from improved bandwidth.

Disadvantages of AGP

Cost:

Video card memory is very expensive compared to regular system RAM.

Limited Size:

The amount of memory on the video card is limited: if you decide to put 6 MB on the card and you need 4 MB for the frame buffer, you have 2 MB left over for processing work and that's it (unless you do a hardware upgrade). It's not easy to expand this memory, and you can't use it for anything else if you don't need it for video processing.

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