To enable faster processing in gene sequencing, you need Software Tools to program in multicore

By Robert Langreth and Ryan Flinn – Oct 4, 2012 12:01 PM GMT+0800
Gene sequencing can speed the diagnosis of rare genetic disorders in newborns and find causes of mental retardation in cases with unknown origins, according to two studies that move DNA mapping closer to clinical use.
Researchers at Children’s Mercy Hospitals and Clinics in Kansas City, Missouri, scanned the DNA of sick infants using a new speed-reading method to diagnose rare genetic illnesses in two days instead of weeks, results published in Science Translational Medicine found. Dutch scientists reported in the New England Journal of Medicine how they found genetic answers for 16 of 100 patients with mental retardation of unknown cause.
The new research supports an effort to bring gene- sequencing technology, mostly used in academic, government and company laboratories, into hospitals and doctors’ offices for diagnostic purposes. The studies were made possible in part by technology from San Diego-based Illumina Inc. (ILMN) and Carlsbad, California-based Life Technologies Corp. (LIFE), the two biggest makers of gene-sequencing machines.
“This is the biggest breakthrough in this technology for clinical applications we have seen in a few years,” said David Dimmock, a geneticist at the Medical College of Wisconsin and Children’s Hospital of Wisconsin in Milwaukee, about the study of newborns. “The ability to sequence and interpret a genome in less than week is huge.”
The researchers at Children’s Mercy Hospitals and Clinicscreated software that takes raw data from DNA scanning machines and combs though hundreds of genetic disorders to spot disease- causing mutations. The system provided likely diagnoses for three of four sick babies in about two days.

Practical Use

The new method has the potential to make genome sequencing practical for neonatal intensive care units, enabling doctors to diagnose mysterious genetic diseases more quickly, said Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children’s Mercy and a study senior author. Fast diagnoses of sick babies may lead to life-extending treatments sooner in some or help avoid futile, costly therapies in others.
Dimmock, who wasn’t involved in the study, said researchers at his institution were working on a similar fast genome interpretation system, but hadn’t published the results yet. “They beat us to the punch,” he said.
The colossal volume of raw data generated from gene sequencing must be analyzed by expert genetic researchers, a process that previously has taken weeks or months.

Smart Software

Kingsmore and his team tackled that issue by devising smart software that allows treating doctors to enter in a sick baby’s symptoms. The software then matches these reported symptoms to known genetic diseases that have similar symptoms, and scans through the baby’s genome results for likely harmful mutations in relevant genes.
“We think this is going to transform the world of neonatology,” Kingsmore said during a conference call with reporters. “Until now, this was just not possible” to get whole genome scan results quickly enough to help sick newborns in intensive care units, he said. “Babies either died or else got better and were discharged home before the results of a gene test were returned.”
For cases in which treatments are available, spotting the cause of a disease sooner may allow treatments to be started before it is too late, he said. Kingsmore estimated the total cost of the test to be about $13,500.

More Data

The software so far includes 600 genetic diseases that affect children, Kingsmore said in a telephone interview. His team plans to have all 3,500 genetic diseases where the precise genetic cause is known entered in the system by the end of the year. There are thousands more genetic diseases where the causes are still unknown.
The projected two-day turnaround for the test doesn’t include the time to express-mail DNA samples to Illumina and for the company to send back the results on a hard drive. Including this transit time, the process took about a week, Kingsmore said. Kingsmore said he hopes to achieve the two-day time after Children’s Mercy gets its own copy of the new Illumina machine later this fall.
Though results from the newborn study “push the envelope,” the two-day turnaround represented a “best-case scenario,” that is unlikely to be achieved in most real-world circumstances, said Wendy Chung, a molecular and clinical geneticist at Columbia University.
A more realistic time for genome results would be a week, given practical considerations such as the fact that most hospital labs close over the weekend, she said. This still would be a big improvement over current methods, she said.

Few Solutions

Chung also cautioned that there only are a minority of cases in which super-fast gene scans will lead to life-saving treatments. Most severe genetic diseases don’t have good treatments, and the ones that do often can be diagnosed by other methods that don’t require every gene to be scanned.
The study was sponsored by Children’s Mercy and the Marion Merrell Dow Foundation. Illumina provided free DNA sequencing for the babies in the study and several of the company’s researchers were co-authors on the study.
In a separate study, Dutch scientists sequenced the genomes of 100 individuals with mental retardation with no known cause and found genetic reasons for 16 of them.
While more than 400 genetic mutations are known to cause intellectual disability, they are responsible for less than half of the cases, said Han Brunner, a study author and head of human genetics at Radboud University Nijmegen Medical Centre in the Netherlands.

Improved Diagnoses

The study shows how gene sequencing can improve diagnosis in patients with mental disabilities. Knowing the genetic origin can help patients and families understand the prognoses and may lead to specific treatment options, the authors said in the study.
“Half of the children and adults with intellectual disability never have an explanation of why they are retarded — that’s a big problem,” leading many parents on a quest to numerous doctors looking for answers, Brunner said in a telephone interview. “This is what people call the diagnostic odyssey, and people can put that to rest,” by using genetic sequencing, he said.
Researchers scanned the DNA of children with mental retardation, defined as having an IQ of less than 50, as well as their parents, and looked for differences. While all children have some mutations, few lead to intellectual disability, Brunner said. Once the culprits are known, it can help direct some therapies or dietary changes.
“We had two cases where the type of mutation would suggest that you might try a treatment for a
metabolic disorder, and another with epilepsy,” he said.

For instance, patients with a mutation in the PDHA1 gene would benefit from a ketogenic diet, which is high in fat, and those with SCN2A mutation should avoid sodium-channel blockers to better control their epileptic episodes and improve cognitive function, according to the study, which was sponsored by the European Union.
To contact the reporters on this story: Robert Langreth in New York at rlangreth@bloomberg.net; Ryan Flinn in San Francisco at rflinn@bloomberg.net
To contact the editor responsible for this story: Reg Gale at rgale5@bloomberg.net

Typical processes for programming multitasking

Typical processes for programming multitasking

A person who travels from Outram MRT to Boon Keng MRT this is what will happen ;

Camera 1
Scans customer facial features
Gate 1 (Entrance)-Outram MRT
Customer taps card at Gate 1 where his details is captured
Train XYZ arrives
Now there will be a separate process to control the movement, stopping, door opening and closing of the train which I will not elaborate because it will complicates the programming.
Camera 2 (At train entrance)
If customer leaves train platform and head for an authorised exit, the security warning will sound, if not, process will continue 
Customer enters train and train door closes, makes announcement before it leaves the platform

At Boon Keng MRT train arrives
Camera 3 (At train entrance)
Scans customer who will leave the train exit
Customer will leave the train and head for the exit
Camera 4 (At train exit)
Scans customer who will leave by the gates
Gate 2 (Exit)-Boon Keng MRT
Customer taps card and the amount of the trip is deducted

End of process.

This is a typical very basic scenerio which needs to be documented so that when you start programming, you will know exactly if there are mistakes and start troubleshooting. If such a view you do not have, you will screw up everything and nothing will come to completion. The security camera operation is 100% more complicated and if you do not have all the processes, you can not separate the tasks for multicore processing and everything will come out garbage like Windows XP or 7. Imagine if every entrance is monitored, how many camera will there be in a station?
Figure how complex is the program if you need to monitor every facial expression, voice recognition with routines for every passenger, break points to run other processes and almost a million passengers, at every camera point. Without research and funds, there will be no solutions because you need to separate trillions of processes between hundreds of the fastest computers in a server farm, no one in america is capable to assemble the lines of code and processes. Not only that, I need to invent intelligent programming with intelligent OS then I have the capability to solve this enormous task. Even the present hardware cannot handle the tasks. This is as complicated as linking all the worldwide exchanges together, america do not have the technology now. You need to monitor every single process for multitasking and proper execution of codes until completion with error correction and loops, with the ability to lock your threads, and nobody has invented this yet. America cannot trick me to review my secrets because you need to invent 100s of new technologies to achieve my goals, it will take another 200 years, nobody can play games with me.
I can easily breakdown any processes, separate and reassemble anything I want into multiple views and scenerios, even black boxes, creating my own technologies.

– Contributed by Oogle.

CSI investigation by tracking and monitoring usage to detect unusual activity, where it is possible to identify using the digital footprint

AsiaOne
Saturday, Oct 20, 2012

SINGAPORE – A woman who had close to $7,000 stolen from her bank account can heave a sigh of relief as the bank has agreed to help compensate for her loss, Lianhe Wanbao reported on Friday.
United Overseas Bank has agreed to pay Madam Lee back after funds from her account were illegally withdrawn from an automatic teller machine (ATM) in the Philippines.
According to the Chinese daily, someone had withdrawn money from the account about 20 times on October 14 and 15. The amount taken out each time was about $300.
It is believed that information had been stolen by a card-reading device when the card was used in Singapore.
A fraudulent card was then created with the stolen information and used at an ATM in the Philippines.
Security measures put in place earlier this year in response to a largescale DBS ATM fraud case had made it more difficult for ATM cards to be used overseas.
However, the victim had earlier applied for her card to be used overseas.
A spokesperson from UOB told Lianhe Wanbao that Madam Lee was notified of the discrepancy as soon as unusual activity was detected.
UOB also said that it held the security of bank accounts with high regard, and advised all bank account holders to change their personal identification numbers regularly to protect themselves from theft and mischief.
ljessica@sph.com.sg
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CSI investigation by tracking and monitoring usage to detect unusual activity, where it is possible to identify using the ATM’s CCTV, the criminal would have left evidence of a digital nature while using the forged ATM card, the evidence can be found on the magnetic stripe, which will be similar to the skimming machine, and can be traced back via the database of the bank’s customer usage, the breakdown of the tables of the database holds the key, it is therefore possible to spot the difference between the original and the duplicate, by looking into the digital footprint which will defer from the original, and the exact breakdown of when the breech occur at which ATM branch, by comparing the date, time of all digital footprints. The work is like tracing a bullet that is fired to which gun, and there is only one match. The trick is to look at the molecular breakdown of the media.
– Contributed by Oogle.

How to tighten security on your computer

How to tighten security on your computer

1) Your browser is the greatest security threat if you are using IE as one can attack you using active X, if you are using other browsers, your add-on is also a way to compromise your pc, there are so many ways to trick you to access your cache data from your browser which contains your ID and password, even your temporary files of your browser can be easily compromised.

2) The greatest security flaw is for webmasters to embed codes into your pictures and videos which you download from their webpages, it is a known fact among the elite, which can easily extract info from your computer, if the person wants to furthur his agenda, there is no way you can stop him, because there is no defence.

3) For SSL security, everything is encrypted when you download from a secure website, which it is almost impossible to hack, there is a risk of man-in-the-middle attack if you security token is not high enough, my advice is use the highest encryption possible, so if they are able to intercept, they will not be able to unencrypt. Even for a secure website, sometimes website do not secure their database, where their database ID, password is exposed, it is possible then to compromise, I can attack the database without using their webpages, and exposed the tables and its contents.

4) It is possible to hide your DNS servers against DDOS attack, the trick is not to accept connections from suspected IPs, so it is possible to have a database of IPs that will reject connections, you can query an IP address before you accept connections, it is even possible to have a DNS server to be only visible to a range of IP address, so that those on the list can see the DNS server and accept connections, the domain names are linked to a specified IP, or can be fowarded to a secure zone which only accept specific range of IPs, the idea is to automate the processes that only allow the DNS server to be visible on a certain time frame for access eg during the promotion of an event.   

5) The greatest security secret is that powerline technology if you do not encrypt your powerline, it can be compromised without anybody knowing, nobody wants to tell you the truth, and if you are doing secret research work, it will be easy prey.

6) The highest level of security for antivirus software at present is found in Norton 360, which will stop the virus on its tracks once it is detected as a threat, which most other vendor’s antivirus will only stop the threat after the damage is done, others compare it with a known database, if it is unknown the virus will not be detected.  

I will not show you exactly the method of penetration, as I do not believe in ethical hacking, by giving the public the method I will create a huge number of hackings, will I do not want, the best is to leave it to security experts to find out what I am talking about. Even without source codes I can monitor and observe all the processes, the applications it spurs, and the results with great accuracy to find all the answers I need. Use XP as a base to observe all the functions in Maintenance and Admin Tools, Windows Task Manager, Msconfig, all the processes, the different apps it spurs, to know what I am talking about, because with Windows7, everything is hidden. Every application I want to learn, is naked before my eyes, and after 10 years of learning, everything becomes chicken feet. 
– Contributed by Oogle

Developing the Next Generation Software without Sourcecodes

I have broken the barriers,
And it is now possible,
To develop new software,
Without looking at the Source Codes.
The Secret lie in testing and comparing,
Against the objectives of the software,
Every application and its goals,
Every way it handles objects,
Every technology,
Then compile to provide,
The view to the entire Roadmap.
It is not possible to be perfect,
But by doing it you will learn and understand and develop,
The next generation software.
Without breaking the Source Codes.
———————————————————————————————————-

The Freeing of Intellectual Property

Most people are not aware,
By freeing Intellectual property,
And licensing such,
If a new product or technology is created,
You will have a share in it,
Is the greatest model,
To maximise your returns,
We are on the very verge,
Of converging technogies,
Where hardware is more advance than software,
But in time to come,
Software will advance in quantum leap,
And overtake hardware,
I will provide the designs,
The models and the visions,
Of taking Software so advanced,
That by testing the limitations of software,
And finding the solutions,
It is possible to design,
The next possible chip and computer,
To handle the new software.

Contributed by Oogle.

Increased security to deny access to cyberattack

“Ubuntu 11.10 Desktop(32bit) installation CD has been compromised where the folder contains ram0-15 and tty0-62 where they sent screenshots to a maximum of 62 terminals with total control of your keyboard and mouse although it does not contain a key logger which will give it away. Windows desktops seem to be hit with an unknown virus which is even higher than flame virus capabilities and I am still trying to track it down. It seems the creators are targeting me and my research, accessing even my contact lists in my mobile.  The flame virus needs to hop from pc to pc, so it will leave a trail behind even if it deletes all traces from the attack pc, so with network monitoring tools, I can capture and isolate it. The problem I found is attack from suspicious websites which uses code to activate your browser plug-in, sending all activities to a specific website. – Contributed by Oogle.”

IMRWorldwide.com is suspected of possibly being a scam or site engaged in fraudulent activity. Although this has not been verified, below are some community projects watching fraud that may have further information about IMRWorldwide.com.

– Contributed by Oogle.”

Posted: 08 June 2012 1350 hrs
TALLINN: Quick advances in cyber war technologies could soon lead to a new generation of so-called “intelligent cyber weapons” which top global IT defence experts warn could be virtually unstoppable.
“Rapid developments in cyber (technology) might lead to intelligent cyber weapons that are hard to control and it’s practically impossible to use formal methods of verifying the safety of intelligent cyber weapons by their users,” Enn Tyugu, IT expert at Tallinn’s NATO Cyber Defence Centre said at its fourth annual conference on Thursday.
He also warned that programmes developed to counter attacks by malwares like Stuxnet can act independently and could possibly themselves spark conflicts.
“They are quite autonomous, and can operate independently in an unfriendly environment and might at some point become very difficult to control… that can lead to cyber conflict initiated by these agents themselves,” Tyugu said.
“Stuxnet and Flame have shown the side of cyber of which the average user does not think of but which will bring a lot of challenges to all experts who deal with critical infrastructure protection issues – IT experts, lawyers, policy makers,” Ilmar Tamm, Head of the NATO Cyber Defence Centre told AFP on Thursday.
“The number of cyber conflicts keeps rising and it is important to understand who the actors in these events are, how to classify these events and participants, and how to interpret all that,” Tamm said, noting Western leaders have been slow to become aware of even existing cyber threats.
Experts at the conference noted that both China and Russia have significantly upgraded their cyber-defence capabilities in recent years by creating new IT units.
“But the most powerful weapon today in cyber space is still the propaganda, the chance to use the Internet to spread your message,” Kenneth Geers, US cyber defence expert told some 400 top IT gurus attending the meeting Thursday.
Keir Giles, head of Oxford University’s Conflict Studies Research Centre, noted that some Russian leaders seemed to “sincerely believe that the recent opposition rallies after the presidential elections in Russia were initiated by the US in cyberspace.”

– AFP/al
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You can protect against the risks of cyberattack by securing these access;
1) No mobile access for places where security is vital, even using jaming devices to create a field where no mobile devices can be used.
2) Secure powerlines using encryption where even the power supply to computers is restricted and also internet access by encryption of all access. Do not use wireless.
3) A gateway monitoring software eg the latest firewall technologies
4) Point-to-point encryption software
If you cover all of the above, there is virtually zero chance of a cyberattack, if someone is trying to access thru the internet to your pc, then just cutoff your internet access temporary by employing monitoring software.
The greatest security breech is that using powerlines via your computer power supply, someone can access your computer even if you do not have internet access. It is using an unknown technology via an unknown protocol. That is the reason you can run but you cannot hide, only this way you can erase every evidence of breech, if you attack by the internet, you will leave your trail, because you need to hop from pc to pc, even if you erase everything on your compromised pc. The easiest attack is to overheat your computer, cause a blue screen, and insert malicious code into your computer. Therefore there will be a great demand for an IT firm to produce encryption software to tunnel your communications from point to point.

Homeplugs (Only the link between Homeplug devices is encrypted) Manufacturers should redesign the Homeplug to even protect the power supply to the PC

Since signals may travel outside the user’s residence or business and be eavesdropped on, HomePlug includes the ability to set an encryption password. The HomePlug specification requires that all devices are set to a default out-of-box password — although a common one. Users should change this password. On many new powerline adapters that come as a boxed pair, a unique security key has already been established and the user does not need to change the password, unless using these with existing powerline adapters, or adding new adapters. Some manufacturers supply adapters with security key buttons on them, allowing users to easily set unique security keys by plugging each unit in one at a time and pressing the button on the front (see more detailed instructions that come with the units).
To simplify the process of configuring passwords on a HomePlug network, each device has a built-in master password, chosen at random by the manufacturer and hard-wired into the device, which is used only for setting the encryption passwords. A printed label on the device lists its master password.
The data at either end (Ethernet side) of the HomePlug link is not encrypted (unless an
encrypted higher-layer protocol such as TLS or IPsec is being used), only the link between HomePlug devices is encrypted. The HomePlug AV standard uses 128-bit AES, while the older versions use the less secure DES.

Since HomePlug devices typically function as transparent network bridges, computers running any operating system can use them for network access. However, some manufacturers only supply the password-setup software in a Microsoft Windows version; in other words, enabling encryption requires a computer running Windows [1]. Once the encryption password has been configured, Windows will no longer be needed, so in the case of a network where all computers run other systems a borrowed laptop could be used for initial setup purposes.
MPPE (Microsoft Point-to-Point Encryption) Shouldn’t it be free bundled with your Windows 8?
Microsoft Point-to-Point Encryption (MPPE) is a protocol for encrypting data across Point-to-Point Protocol (PPP) and virtual private network (VPN) links. It uses the RSA RC4 encryption algorithm. MPPE supports 40-bit, 56-bit and 128-bit session keys, which are changed frequently to improve security. The exact frequency that the keys are changed is negotiated, but may be as frequent as every packet.
MPPE alone does not compress or expand data, but the protocol is often used in conjunction with Microsoft Point-to-Point Compression which compresses data across PPP or VPN links.
Negotiation of MPPE happens within the Compression Control Protocol (CCP), a subprotocol of PPP. This can lead to incorrect belief that it is a compression protocol.

– Contributed by Oogle. 
 

New antenna that increases Wi—Fi speed by 200 times

Updated: Tue, 28 Aug 2012 17:29:51 GMT | By Channel NewsAsia

SINGAPORE: Researchers from A*STAR’s Institute of Microelectronics (IME) have developed the first compact high performance silicon—based cavity—backed slot (CBS) antenna that operates at 135 GHz.
About the size of a sesame seed, it is the smallest silicon—based CBS antenna reported to date for ready integration with active circuits.
IME’s innovation will help realise a wireless communication system with very small form factor. It is almost two—thirds cheaper than a conventional CBS antenna.
The antenna can support wireless speed of 20 Gbps — more than 200 times faster than present day Wi—Fi.
This means there will be ultra fast point—to—point access to rich media content which is useful in online learning and entertainment.
— CNA/cc