BioInformatics Reviewed Links

BioInformatics Reviewed Links

Link: http://www.bitlaw.com/patent/requirements.html

Reviewed by: Rajiv Kumar

ÝÝÝÝÝÝÝ PATENT REQUIREMENTS

This web page lists patent requirements and conditions for invention or

discovery of any new and useful process, machine, manufacture, or

composition of matter, or any new and useful improvements. To patent an

invention, it lists four requirements viz. Statutory Requirement,

Novelty Requirement, Usefulness Requirement and Non-Obviousness Requirement.

Statutory requirement follows the US Patent Statute which states that

processes, machines, articles of manufacture and compositions of matter

are patentable. Recent rules issued by the USPTO in connection with

software patents states some items to be non-statutory and thus non-patentable.

These include data structures or programs, compilations or arrangements

of non-functional information or a known-machine readable storage medium

encoded with such information, natural phenomena such as electricity

and magnetism because of their indistinguishablility from abstract ideas

and laws of nature. In addition to that, business methods and mere printed

matter are also considered non-patentable.

Novelty requirement requires an invention to be new, to be patentable.

In other words, this requirement states that an invention cannot be

patented if certain public disclosures of the invention has been made or if the

invention was described in publication more then one year prior to the

filing date or if the invention was used publicly, or offered for

sale to the public more than one year prior to the filing date.

Usefulness Requirement specifies that the subject matter must have a

useful purpose which includes operativeness, to be granted a patent.

Non-obviousness requirement specifies an invention to have non-obvious

improvement over the prior art, in addition to being novel. The

invention is compared to the prior art and a determination is made whether

the differences in the new invention would have been obvious to a person

having ordinary skill in the type of technology used in the invention.

Link: http://www.cs.berkeley.edu/optical/

Reviewed by: Changyou Yu

ÝÝÝÝÝÝÝ Optics and Topography Involving the Cornea And LensÓ

This is the web page of the University of California, Berkeley

Describing the research project of optical visualization. The research is

conducted by an interdisciplinary group led by professor Brian A.

Barsky and professor Stanley A. Klein involving members of the Computer

Science Division, School of Optometry and Vision Science Group at Berkeley. The

goal of this project is to develop new geometric modeling and scientific

visualization techniques for curved optical surfaces which will benefit

researchers and clinicians in the fields of optometry, ophthalmology,

and vision science.

This project includes 3 major parts:1) Recovery of corneal shape from

video-keratograph images. A video-keratograph is a device which is used

to project a pattern onto the cornea and record the reflected image. The

image is then analyzed to directly recover the shape information and

produces a continuous map over the entire surface; 2) Visualization of

corneal shape. To display the results from the first part in a manner

that highlights the important features of the surface and is understandable

to viewers with a wide variety of backgrounds, a number of different

visualization techniques have been investigated, some of which are based on 2D

images, whereas others fully exploit the 3D graphics capabilities of current

workstations; 3) Design of personalized and complex contact lenses.

With the improved method for finding corneal topography, the researchers

have opened the way to develop contact lenses that are more precisely

designed with an individual's cornea.

With computer aided geometric design knowledge, the research group

feels confident to develop the contact lens of the future.

Link: http://www.gisdevelopment.net/application/lbs/lbs003.htm

Reviewed by: Xiaodong (Sheldon) Zou

ÝÝÝÝÝÝÝ Mobile Geographic ServicesÓ

This site introduces a new breed of mobile

geographic application services that is being

developed by ERRI and shows how to build a

geographic system.

Mobile geographic application, which supports

itinerant, distribute, ubiquitous computing, can be

performed at different places in a way that is

transparent to users and delivers the same

functionality independent of a users location. A

service is a server-based application that delivers

data or processing to clients on demand. Geographic

services receives requests from clients ( pagers,

phones, Pocket PCs, PCs, etc.) for geographic data

or processing ( make a map, geocode an address,

download data for an area ) The result could be

displayed to the client. When a client chooses the

service, the mobile information system can also know

where the client is.

A mobile geographic system ( GIS ) is a system

built using a fundamentally new paradigm based on

the key element that includes Wireless Network,

Client Device, Application Data and Date Server.

Many methods of wireless communication are available

to mobile geographic system including radio

communication. Advancement in hardware performance

have allowed of small, low-powered devices suitable

for mobile geographic application. A critical part

of a mobile GIS is an advanced geographic

application server able to provide a range of

geographic services. The final component is a

geographic containing the content that will be made

available via the geographic services in the

application server.

 ESRI company has been building GIS software for

many years. The heart of ESRIs mobile geographic

services is a commercial off- the-shelf solution

called ArcGIS which satisfies the needs of desktop.

ESRI also offers both client centric and

server-centric geographic service solution.

Server-Centric solution:

ESRI company's mobile geographic services

solutions are based substantially on AarIMS that is

a cross platform application server.

Client-Centric solutions:

A second key piece of ESRI software for

mobile geographic solution is ArcPad which is a

relatively lightweight commercial off the shelf GIS

application.

The author told us that mobile geographic

service is a fast growing field of GIS. It is clear

that even today technology is finding and business

benefits in geographic information in a mobile

context. ESRI has been building mobile geographic

services for a number of years based on the

well-tried and tested ArcGIS technology. Key aspects

of the ArcGIS systems are the ArcIMS application

services provider and ArcPad, the lightweight mobile

GIS client for Pocket PC devices.

Link: http://www.axph.com/technology/compdesign.html

Reviewed by: Xiaodong (Sheldon) Zou

ÝÝÝÝÝÝÝ Computer-Based Drug DesignÓ

Computational tools have become increasingly

important in the drug discovery and design

processes. In this link, Axys Pharmaceuticals Inc

provides a good background reference to understand

Computer-Based Drug Design technology.

It begins with the effort to map and sequence the

human genome. Scientists to identify the 100,000 or

so genes that make up the 23 pairs of chromosomes

that instruct our bodies how to grow and reproduce.

At the same time, they are moving rapidly to

sequence the 3 billion "base pairs" of DNA that make

up the chromosomes. The purpose is to create a

complete "reference" human genome that will guide

researchers through the complex inner workings of

chromosomes and genes and provide tools for further

studies of fundamental human biology and disease.

These technique include positional cloning, which

allows scientists to map and sequence specifically

those genes related to disease.. This is an

invaluable new tool in drug discovery because many

common diseases are caused by more than one gene, the

ability to identify the locations of the genes to

sequence their DNA, and to track the interactions

between the genes and their protein products, requires

the ingenuity of the best data base programmers in the

world.

Gene chip" technology represents another important

advance in the effort to delineate DNA sequences and

gene function. Specially built and programmed

computer chips have been invented that can

physically interact with DNA samples to evaluate the

expression levels of thousands of genes

simultaneously. This technology can reveal valuable

information about the differences between the

expression patterns of normal and diseased genes and

the protein products of the genes that play a role in

disease.

Once a disease target molecule is identified-

typically a protein that operates at a critical

point in the disease pathway, computers and

computer-operated robots are essential to the

process of screening the molecules and tracking the

large volume of data generated by high throughput

screening.

Finally, any drug candidate chosen to proceed

into human clinical trials will have graduated

through a series of experiments devised and

monitored to a great extent by computers. Once a

drug goes into trials, the use of computers in no

way diminishes. Robust and sophisticated data base

capabilities are essential to tracking everything

from basic patient information to side effects

profiles. New advances in the field of

pharmaco-genomicsð may change the entire nature of

clinical trials themselves. In fact, at each step

along the drug discovery process, computers have

helped transform rate-limiting factors into

opportunities for realizing new drugs more

efficiently.

Link: http://www.sciam.com/news/092001/1.html

Reviewed by: Tawhidul Chowdhury

ÝÝÝÝÝÝÝ First Complete Trans-Atlantic Robotic SurgeryÓ

This article introduces a new technique for surgery using remotely

controlled robot which is done by surgeon in New York from where the

patient is 7000 Kilometers away in France. This is the first complete

Trans-Atlantic robotic surgery. The surgeon removed a 68Òyear-old

womanÌs gallbladder by simply sitting at a computer console here in the U.S

while the patient was laid far across the Ocean from the surgeon. The surgeonÌs

hands movements are transmitted via a hi-speed fiber optic connection to the

robotic hands that are in contact with the patient. The surgeon can

watch his hand motions 155 milliseconds later from the actual time of the

movement on a video screen

The advantage of this technique is that the robot can perform minimally

invasive operation which uses a thin tube equipped with a camera, and

surgical instruments are inserted into a patient.

There are some disadvantages with this tele-surgery. Latency problem is

created by the video can risk the patient. The scientist has to develop

high-quality video and wired with enough bandwidth to handle the

information necessary for the remote surgery. Earlier experiment shows that this

remote surgery is very dangerous for the patient because the period from when

a surgeon moves his hand to the moment the scalpel mimics that motion

cannot be delayed more than 330 milliseconds; otherwise the surgeon risks

slicing at the wrong spot. It is extremely important to transmit data very

efficiently to keep tele-surgery real-time.

Another problem related with this tele-surgery is that it is very

costly. Even for robot-assisted surgery done in the same place, the cost is

very high because the system not onlyð contain pricey hardware, but they

required trained support staff. For example, some one who has skills about the

robotic surgery has to set up the equipment and the robot itself and

has to watch to take over at the first sign of trouble.

Link: http://optics.org/article/news/7/11/30

Reviewed by: Tawhidul Chowdhury

ÝÝÝÝÝÝÝ Optical tweezer set for launchÓ

The article reports on the space tweezer that will be installed in the

International Space Station to study the colloid crystallization in a

micro-gravity environment.

The space flight tweezer is different from ground based tweezer by size,

power consumption and the need to operate without human intervention.

The tweezer unit is part of a microscope. The size of this tweezer is

small, and power consumption is very low.ð The total area of the tweezer setup

system is about 30cm X 30cm X 10cm. The setup system composed of a

continuous-wave laser, a deflector for beam steering, two lenses for beam expansion and

imaging, two polarisers to control the beam intensity and trapping

strength; and two mirrors to shrink the overall package size. It is fully

automatic, and it can operate without human.

This space tweezer consists of a strongly focused laser beamð which has

the ability to catch and hold particles of dielectric material in a size

range from nanometer to micrometer. For example, this technique of using

laser beam makes it possible to study and manipulate particles like atoms,

molecules and small dielectric spheres.

The tweezer has a specific set of samples consist of micron-sized

polymetheyl methacrylate spheres and functions to examine the structure

of the particular state of the colloid. It can also manipulate the result

of the colloid crystallization. For example, a defect can be created by

removing a particle or dislocating row of particles and the effects of

this defect on the crystal properties can be deduced. Andy Resnick, a

spokesperson for Northrop Grumman, US, under contract toð NASA, said

that the partial result of this kind of defect would be transmitted back as

the experiment proceeds, and a lot of data would simply be stored on hard

drives and brought back to Earth.

Link: http://www.photonics.com/Spectra/Tech/Feb00/techBiosensor.html

Link: http://www.lanl.gov/worldview/news/releases/archive/99-166.shtml

Reviewed by: Gang Pan

ÝÝÝÝÝÝÝ A Portable Fluorescence BiosensorÓ

The above web sites describe the new development of a portable and

sensitive fluorescence biosensor, based on quenching in a conjugated polymer, to

identify a variety of pathogens or biological agents almost instantly.

It was made by researchers at Los Alamos National Laboratory and the

University of California at Los Angles. A biosensor can detect presence or

concentration of biological agents, biological structures and viruses

by converting a biochemical reaction to a measurable signal. Some

polymers e.g. fluorescence can be quenched after they transfer the electrons

to the agents/receptor sites under laser irradiation.

Researchers have designed a reaction process analog to a lock and key,

which can be described as follows: a) a specific ligand attaches to the

polymer to quench the fluorescence; b) the molecular package then gets away from

the new polymer by the analyte. The analyte include pathogens, proteins,

viruses and bacteria. The ligand part, called a quencher-tether-ligand (QTL)

like the key, whereas the analyte is similar to the lock. It is very

important to bind the quencher to the analyte selectively and strongly, which can be

solved by attaching a ligand to the specific quencher. Key advantages

of the new technique include non-separation, rapid speed and instantaneous

analysis, making it competitive with existing biosensor detection

systems.

The sample will be held in either a small vial or on the tip of an

optical fiber and the data will be processed by a laptop computer, which make

the device as simple as possible.

The novel and lightweight biosensor has generated considerable interest

from medicine and clinic, as the potential applications in diagnosing

diseases such as influenza and HIV or detecting specific drugs. Their next

objective is to use the technique in other biologically relevant systems,

including blood, urine and other bodily fluids.

Link: http://www.nytimes.com/2001/11/27/science/physical/27ROBO.html

Reviewed by: Tawhidul Chowdhury

ÝÝÝÝÝÝÝ Robots Learn Soccer and the Game of Life

The article reports on how Robot can be used as the bestð model to

represent the nature of human behavior. In this review, Dr Balch, a robotic

researcher at the Georgia Institute of Technology in Atlanta, said his experiments

could provide surprising insights into the working of human society.

His plans is to reproduces his experiments using the real robotsð that will

bring his findings closer to the domain of social reality.

The robots learn to play soccerð by executing a random sequence of

basic moves. For example, the robots can run toward the ball, kick the ball,

move behind the ball, and block the ball. Dr. Balch divided his robots into

two teams. The robots on a control team are able to pass the ball, defend

and attack from the starting whistle. The test team must learn by trial and

error as the game progresses. His program can reward and punish the

robot depending on whether the sequence made sense or not. The reward signal

is sent to all members whenever any robot scores a goal. Therefore,

control team and test team behaves much differently. Dr. Balch said, Group

rewarding produced greater diversity and made the team a wining combination.

Although the robots act much like human when they play soccer, it is

very hard to implement robot with human complexities. For example,

motivation and jealousy are impossible to reproduce in robotic system, but his

experiment shows that robot studies can serve as a window for understanding human

behavior.ð For example, if a reward signal is sent to only one robot

that scores a goal, every team members ends up learning the same sequence of

behavior. The robots go after the ball in a solo effort to score in

order to achieve the reward. Competition for rewards pressures people, just like

robots to act very similarly, said, Dr. Roger T. Johnson, who studies

cooperative learning at the University of Minnesota. He also said,

similarly,ð cooperative reward system produces similar behavioral

effect on both human and robots.

In this article many other social scientists seem to disagree with the

BalchÌs idea of parallelismð between human and robot, BalchÌs

experiment on robots indeed shows a greatð similar behavioral effect between human

and robots.

Link: http://www.stanford.edu/group/pandegroup/Cosm/BHvijay.pdf

Reviewed by: Christopher Conway

ÝÝÝÝÝÝÝ Distributed Computing Simulation of Beta-Hairpin Folding

Vijay Pande's group at Stanford University is working on large-scale

distributed computing models of protein folding. This paper describes

the data produced by using their distributed simulation system to model

the folding of the C terminal beta-hairpin from protein G. A beta sheet

is a commonly occurring protein secondary structure composed of two or

more extended polypeptide chains with hydrogen bonds between them. A

beta-hairpin is a motif connecting two chains in a beta sheet -- it is

a tight bend (thus "hairpin") typically consisting of two to five

amino acids. The folding characteristics of beta-hairpins in general,

and the C terminal beta-hairpin from protein G in particular, make

them an ideal starting point for modeling the folding of more complex

structures.

The key insight in this experiment is the computations required to

explore the state transitions of the molecule are parallelizable and

that distributing the work to M processors will result in an effective

speed-up of roughly M times. This allowed the researchers to compute

38 microseconds of folding time. The calculations revealed eight

independent folding patterns and several important interactions and

intermediate states.

Link: http://www.sigmaxi.org/amsci/amsci/issues/comsci01/compsci2001%2D05.pdf

Reviewed by: Christoforos ChristoforouÝÝÝÝÝÝÝ

ÝÝÝÝÝÝÝ Computing comes to life

This report discusses research that is been done in

using biological components as building blocks for

computer systems.

Current computer technology is based on

transistor-to-transistor Logic. Transistors are

connected in different ways to implement logic devices

like AND gates, OR gates and NOT gates. These logical

gates can operate to signals with two possible values,

either true or false. An AND gate takes two or more

input signals and outputs true only if all the input

signals are true. An OR gate takes two or more input

signals and outputs true if at lest one input signal

is true. A NOT gate is the simples of the logical

gates and it outputs true if the input signal is false

and vise versa. The goal of biocomputing is to turn

cells to computer starting by implementing the

building blocks of computers, the logical gates, using

cells.

In achieving this goal a special repressor proteins

are used. Repressor proteins if exist in the nucleus

of the cell are bind on the DNA downstream of the

promoter region and stands in the way of the

polymers. This way it prevents DNA code to be copied

on the mRNA and consequently prevents the development

of the protein that is being encoded by the cells

nucleus. If the protein encoded by the cell is itself

a repressor protein (different than the one that was

used and input) then the cell can be thought of a

logical NOT gate. If a repressor protein A exists

(Input true) in the cell that encodes repressor

protein B then the protein A will bind on the DNA

and prevent (Output false) the development of protein

B. If, on the other hand, repressor protein A

exists (Input False) then the protein B will be

produced (Output true) and since protein B is itself

repressor protein it can be used as input to some

other logic gate. Similarly all the other gates can be

constructed base on the same idea and combined

together to form more complicated circuits.

Problem with using this approach is the fact that

every cell must encode different repressor protein and

since a circuit is usually composed of millions of

logical components finding such number of distinct

proteins is difficult. Further, the problem of

possible infection of cells is being considered.

Link: http://www.uphs.upenn.edu/ihgt/info/whatisgt.html

Reviewed by: Christoforos Christoforou

ÝÝÝÝÝÝÝÝÝÝÝÝÝÝ

ÝÝÝÝÝÝÝ Gene Therapy

This document discusses gene therapy as a method for

treating gene level deficiency diseases.

Abnormal cell behavior is often due to an altered gene

whose expression is either absent or unregulated.

These altered genes can cause the synthesis of

problematic proteins. Gene therapy goal is to deliver

to the cell a correct version of the gene, the

expression of which will produce a normal protein and

hence correct the problem.

Delivery of the correct genes to the altered cell is

achieved by the use of some delivery vehicles, called

Vectors. The goal of these vectors is not only to

deliver the corrective gene sequences to the cell but

also copy the genes to the hosts cell chromosomes.

Some viruses, members of retroviruses family, are able

to do exactly that, to get into the nucleus of the

cell and copy their genes to the hosts cell

chromosome. This property of retroviruses makes them

ideal to be used as vectors. Retroviruses are gutted

of its genes, disposing of those that can be harmful

to the cell and replacing them with the corrective

genes to be delivered. These retrovirus genes that

enable it to insert DNA into chromosomes are kept.

Trials of human gene therapy are currently applied

using two different strategies named ex-vivo and

in-vivo. In the first approach the patient cells are

harvested and cultivated in the laboratory and then

incubated with vectors that introduce the therapeutic

genes. The cells are then transplanted back to the

patient. In the in-vivo process the vector is directly

administered to the patient.

Link: http://www.ultranet.com/~jkimball/BiologyPages/R/Retroviruses.html

Reviewed by: Christoforos ChristoforouÝÝÝÝÝÝÝÝÝÝÝÝÝÝ

ÝÝÝÝÝÝÝ Retroviruses

This paper discusses retroviruses and the way they

infect the cells.

Retroviruses are viruses whose genome consist of RNA

not DNA. RNA synthesized by nucleotides similar to

DNA. These are Adenine, Guanine Cytosine and Uracil

symbolized with the letters A, G, C and U. Uracil is

the respective of thymine nucleotides in the DNA. A

typical retrovirus consist of an envelope protein, and

a protein shell named capsid that contains two

molecules of RNA and molecules of the enzyme reverse

transcriptase. This enzyme reverses the genetic

information flow thus information on the RNA are

copied on the DNA polymer rather that the opposite

which is the normal flow of genetic information. This

enzyme plays an important role to the process of

infecting other cells.

When a retrovirus infects a cell the molecules of

reverse trascriptanse are carried into cell attached

to the viral RNA molecules. The reverse transcriptanse

synthesizes DNA copies of RNA and these copies are

entered in cells nucleus. Some of those DNA copies are

randomly insert themselves on the hosts cell

chromosomes and thus destroying the genetic sequence

of the cell. Some others are transcribed back to RNA

molecules which again part of them are translated by

the hosts cell ribosome to RNA containers and the

rest are incorporated into these newly created

particles.