Showing posts with label opensource. Show all posts
Showing posts with label opensource. Show all posts

Tuesday, January 22, 2008

The 1000 Genomes Project: The Most Detailed Map of Human Genetic Variation

The 1000 Genomes Project: The Most Detailed Map of Human Genetic Variation

Mankind took a major step today as an ambitious effort codenamed The 1000 Genomes Project involving sequencing the genomes of at least a thousand people from around the world was announced in England. The 1000 Genomes Project will create "the most detailed and medically useful picture to date of human genetic variation". Multidisciplinary research teams participating in the 1000 Genomes Project will develop a mapped view of biomedically relevant DNA variations "at a resolution unmatched by current resources". According to the official announcement data from The 1000 Genomes Project will be shared with the worldwide scientific community through freely accessible public databases.

Richard Durbin, Ph.D., of the Wellcome Trust Sanger Institute and co-chair of the consortium

The The 1000 Genomes Project is supported by the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH). Richard Durbin, Ph.D., of the Wellcome Trust Sanger Institute and co-chair of the consortium (in the above photo) explains why this was unthinkable only two years ago:
"The 1000 Genomes Project will examine the human genome at a level of detail that no one has done before. Such a project would have been unthinkable only two years ago. Today, thanks to amazing strides in sequencing technology, bioinformatics and population genomics, it is now within our grasp. So we are moving forward to build a tool that will greatly expand and further accelerate efforts to find more of the genetic factors involved in human health and disease."

NHGRI Director Francis S. Collins, M.D., Ph.D. explains what are the new possibilities may be following this amazing breakthrough:


"This new project will increase the sensitivity of disease discovery efforts across the genome five-fold and within gene regions at least 10-fold. Our existing databases do a reasonably good job of cataloguing variations found in at least 10 percent of a population. By harnessing the power of new sequencing technologies and novel computational methods, we hope to give biomedical researchers a genome-wide map of variation down to the 1 percent level. This will change the way we carry out studies of genetic disease."

The 1000 Genomes Project
http://www.1000genomes.org

Thursday, December 13, 2007

OpenSocial Alliance is here. Social Internet has changed.



It was just the end of October this year when we learned about another open standard alliance led by Google a move that was described as a "FaceBook killer". OpenSocial provides a common set of Application Interface (API) tools for social applications across multiple websites. With standard JavaScript and HTML, developers can now create rich interactive web applications, accessing data from other social networks, update feeds and create new mashed-up content.



Aiming for every social driven and user generated content website out there to implement the new standards, the OpenSocial alliance seek to change the way people are interacting with each other on the internet by removing some of the boundaries set by a chaosed freedom and commercial interests. Websites already implementing the new OpenSocial tools include highly popular websites such as MySpace, Engage.com, Friendster, hi5, LinkedIn, Ning, Oracle and Orkut. Members of the alliance also include Plaxo, Salesforce.com, Six Apart, Tianji, Viadeo, XING and many others. See them all here or check on the video below for interviews with some of OpenSocuial early industry adapters.



Google’s own social network, Orkut, is of course the one that Interests them most but a-la Google's style this is used mainly to give (a limited sandbox for OpenSocial development) rather than take (users from other websites by closing their cross platform communications capabilities). Furthermore, unlike Facebook which uses a proprietary language for their widgets, once you chose developing your new widget with OpenSocial you are totally free to use the best stuff Internet has to offer nowadays including Flash, html and javascript, or in other words - Ajax.



Even though latest figures show the impact on FaceBook's application market is yet minor, the OpenSocial alliance is just one of those things we can't understand how they did not exist until they did and it seems that Google just changed the rules of the game once again. Social Internet has changed. Adding the numbers and including the vast member pool of MySpace - FaceBook's mightiest competitor and an avid OpenSocial integrator - we get a "completely different picture of the combined OpenSocial sites compared to Facebook". A swift look at the above chart posted about a month an a half ago by Bill Tancer, General Manager of Global Research at Hitwise, tells the whole story in short: FaceBook - you took the closed course and got knocked out by the open one. Just like your Microsoft partner.

http://code.google.com/apis/opensocial/
http://opensocialapis.blogspot.com/

Wednesday, December 12, 2007

IE7: "A little over a year". Lots of CSS bugs. Still no bug tracking.

IE7: A little over a year. Lots of CSS bugs. Still no bug tracking.

Well, yes, it has been a little over a year since "they" released IE7 on Windows XP and for Windows Vista, so IE7 Group Program Manager Mr. Tony Chor, who is also an avid blogger, thought "it would be worthwhile to talk about where we are after the year." Why? because of "the positive impact IE7 has made" for Microsoft users, because "as you know" Microsoft "focused a lot on improving security in IE7" making "IE 7 the safest Microsoft browser released to date" and because - yes - "IE7 had both fewer fixed and unfixed vulnerabilities in the first year than the other browsers" they compared with.

Also, says Mr. Chor, "according to internal Microsoft research based on data from Visual Sciences Corporation "over 300 million users are experiencing the web with IE7" making it "the second most popular browser after IE6." I'll save you the rest of the exciting new features and reasons specified by Chor. You can read them all here if you like. The point here is that many angry folks seem to have been waiting a long time for such an opportunity to express their real feelings towards IE7 as well as Microsoft's approach for how to handle their interaction with Internet developer community. I quoted up some of the best onces for you as there are just too many of them. Enjoy.

"Sorry, I can't get past the all-too-frequent IE 7 crashing or hanging at seemingly random times to appreciate anything you just posted." (Internet Explorer has stopped working)

"...It would be sad for IE to fade away in its own delusions of grandeur and support its own misguided standards of how the web should be. Good luck and hope to hear about IE's future developments so I can properly hack my sites to work with its arcane developments." (Joshua)

"From the horrifically god-awful (IE6) to the merely depressingly buggy, nonstandard, and incomplete (IE7)... congratulations!" (Joseph E. Davis)

"... 1 year, still no bug tracking 1 year, still no updates on IE8 features 1 year, still no updates on IE8 bug fixes 1 year, still no ETA on IE8 release 1 year, still no ETA on IE8 Beta release(s) 1 year, still no ETA on IE8 Alpha release(s)" (Sam)

"...Every single day, web authors of all experience, from amateurs to experts/gurus, experience difficulties (from minor to major) with bugs of all kinds in IE 7. When is Microsoft going to finally fix all these proven and testcase-ed bugs?" (Gérard Talbot)

"IE Team called out for biased numbers" (Concerned User)

"I wonder when will you release IE without click to activate..." (n-blue)

"... Let's see... six years for IE7, so you guys are on track to have IE8 by what, 2012? Your problem is you think in terms of years. Your problem is that your company sees the web as a competing platform. Do us all a favor and stop making IE altogether." (Paul)

A few words about my own view. After spending four years with Conceptis development team putting up a totally dynamic yet 100% standard compatible application server there are simply no words to describe how horrible is the fact IE is a closed undocumented software ignoring the fact Internet is not owned by Microsoft:

We had a professional top-gun graphic designer added to our payroll to have the most spectacular GUI ever seen. At least a year was spent on coming up with the basic layout look and language. Aiming to support everyone's Internet experience we took a huge effort to have all of it implemented using 100% W3C standards. We came to a point where IE is supported on the site and design look almost as it should - there is not a single line of code in this project containing the bad behavior of mixing graphic design with code and all graphic instructions are done exclusively via CSS, just as they should be "by the book".

In short, we did our part. Yet, most of the time we spent on CSS development went to solving IE6 particular bugs. There were times when we were certain that eventually we'll bump into all of them, a frightening thought in light of the fact there are hundreds. Now with IE7 around it looks like things are not going to be very different. It looks like we will probably just have to add a bunch of IE7 dedicated hacks to our IE CSS override pool. As explained by a fellow named Gérard Talbot the IE development team still has to fix -

"at the very least 700 bugs, incorrect implementations (all testcase-ed, all demontrable, reproducible) happening in HTML 4, CSS 2.1, DOM 2 interfaces and then implement more or less 500 properties, attributes, methods specified in official W3C Technical Recommendations, W3C web standards (HTML 4, CSS 2.1, DOM 2 interfaces, DOM 2 Core, DOM 3 Core)."

How lovely...

There is one particular comment on this thread which I thought should be brought in full as it pretty much sums up my personal feelings towards the subject discussed. Here it is, exactly as posted on the official IE blog by owner of a web development company Adam Tichy on Thursday, December 06, 2007:

"I'm a web developer, not a literary scholar, therefore I cannot quite find proper words to describe my total disgust with IE. I honestly can't wait long enough for that horrible thing to just crawl into the depths of forgotten projects and die.

"Most of my customers provide consumer or business internet services and they rightfully insist that the web applications work properly in all major browsers. Since MS packages this crap together with the OS it is a small wonder that in whatever diminishing numbers, the IE is still out there in force. It makes my life a living hell! I have to either seriously compromise the design and functionality or essentially build several variants of the sites just to make it work for the ignorant IE6/7 crowd.

And I'm not so sure the smaller number of support calls is something to boast. Judging from the stats on my sites, more and more people access them via the "other" browser(s). If this trend continues (and hopefully it will) you will be receiving even less support calls in the future. 300 million my foot."

[Above illustrative image courtesy of Alex who bumped up a confirmed bug by Microsoft. Confirmed since medieval ages of IE 5.]

Wednesday, November 21, 2007

Redmond, fasten your seat belts: Firefox 3 Beta 1 now available for download



The Microsoft IE7 folks at Redmond must be fastening their seat belts at these moments, getting ready for their largest challenge ever as the world's most superior Internet communication software has just been released as a public Beta. Firefox 3 Beta 1, AKLA 3.0b1 is now available for download with 3 operating systems and more than 20 languages already in supported list.

The rumors about Firefox 3 have been with us for a long time and a lot has been written about the third version. This Internet tool is not going to be just another crappy recycled version of the previous engine with additional bells and whistles and a few "new exciting features" stolen from others and implemented badly (have you seen the exciting new tabs on IE7? how exciting). Firefox 3 is developed as a completely new software, with much of its core re-designed from scratch. The Beta 1 is the ninth developer milestone and includes many new core functionality features and changes to the platform scheduled for Firefox 3 (see 3.0b1 release notes).

New Firefox 3 Beta 1 features:

  • Improved security features such as: Better presentation of website identity and security, malware protection, stricter SSL error pages, anti-virus integration in the download manager, and version checking for insecure plugins.
  • Improved ease of use through: better password management, easier add-on installation, new download manager with resumable downloading, full page zoom, animated tab strip, and better integration with Windows Vista and Mac OS X.
  • Richer personalization through: one-click bookmarking, smart search bookmark folders, direct typing in location bar searches your history and bookmarks for URLs and page titles, ability to register web applications as protocol handlers, and better customization of download actions for file types.
  • Improved platform features such as: new graphics and font rendering architecture, major changes to the HTML rendering engine to provide better CSS, float-, and table layout support, native web page form controls, colour profile management, and offline application support.
  • Performance improvements such as: better data reliability for user profiles, architectural improvements to speed up page rendering, over 300 memory leak fixes, and a new XPCOM cycle collector to reduce entire classes of leaks.

Important notes:

The Mozilla folks say they do not recommend that anyone other than developers and testers download the Firefox 3 Beta 1 milestone release as it is intended for testing purposes only. In addition, If you blog this new further (you should!) please do not link directly to the download site but to this Firefox 3 Beta 1 milestone announcement so that everyone will know what this milestone is, what they should expect, and who should be downloading to participate in testing at this stage of development.


http://wiki.mozilla.org/Firefox3

Wednesday, November 7, 2007

Open Handset Alliance: an Android bad guys did not expect.



The hints kept coming. After unveiling Android, their new mobile phone software, it appears that Google's plans go way beyond another proprietary new software. Instead a consortium of top tier wireless companies is already on the run, developing Android to be "the first complete, open, and free mobile platform" As Linux for mobile still has some troubles gaining an honorable spot, and giving the history of previous Google attempts to move things around, allow me to bet this might work and the world of mobile computing is about to be changed completely.



Companies in the alliance, already counting more than 30, say their purpose is to "accelerate innovation in mobile and offer consumers a richer, less expensive, and better mobile experience" and plan on releasing an access software development kit next week. Yesterday we learned that Federal Communications Chairman Kevin Martin supports Google's Open Handset Alliance saying "more openness, at the network, device, or application level, helps foster innovation and enhances consumers' freedom and choice in purchasing wireless service." More about the new open platform for mobile phones and the Open Handset Alliance in this official video.



According to InformationWeek Google partners include T-Mobile, HTC, Qualcomm and Motorola. "Google is picking holes in the traditional hegemony of telecommunications providers," says Google analyst and author Stephen Arnold. "This is just using what Google's already got. There will be much more to come." Google refer to their Android platform "the first truly open and comprehensive platform for mobile devices."



Google's Android competes directly with other smartphone software available in the market today. This include software from Apple, Microsoft, Nokia, Palm, and Research in Motion. According to CNET the new Android platform consists of "an operating system, middleware, a user-friendly interface, and applications." and we can expect the first Android phones to be purchased sometimes between June to December 2008. There you have it - one Android the bad guys did not expect.



As opposed to mobile operating systems, Android will not be tied to a specific device but will support a long list of devices from major players such as Motorola, HTC, Samsung, and LG as well as Wind River Systems Inc. that joined the alliance as a Linux commercialization partner. A minimum of 200MHz ARM 9 processor is required to run the new system, promised to be "flexible, compatible with small or large screens, keyboards and other input methods."

According to Wikipedia an Android is "a robot designed to resemble a human, usually both in appearance and behavior". The term was first mentioned by Albertus Magnus in 1270 and was popularized by the French writer Villiers in his 1886 novel L'Ève future. I wonder what Magnus would have to say about the new Android.

Saturday, November 3, 2007

Jathia's Wager: Open Source Social Movie Making



The opening scene in the first draft of Jathia's Wager shows a group of people is led by an old man to the edge of a dark forest looking outside into a new world:

EXT. GRASS FIELD - DAY: A dark forest sits at the end of a perfectly maintained sea of grass. Small clusters of buildings shimmer in the distance. A huddled group of people slowly walk through the grass toward the edge of the forest. Their faces turn deadly serious as they get closer to the edge. An old man with flowing gray hair leads the pack. He stops abruptly and holds up a fist. OLD MAN: This is as far as we go.

Change this old man with a young passionate dude, the forest with our existing life and the new world with the Internet and you might figure out the same metalanguage metaphor I see here, as Jathia’s Wager will be no ordinary movie.

Defined as "an open source collaborative filmmaking project" this project invites Internet community to re-interpret, revise, produce, reuse distribute and redistribute a movie for free. Officially announced on July 16, 2007 by Solomon Rothman Films the short Sci-Fi is planned to be telling the story of a "young man living in an isolated community of humans, who must make a life changing decision about his future and his species."

Other than being a cool movie buff and an avid blogger, Solomon Rothman is an American filmmaker living at Los Angeles who has already used the new challenges of online video revolution and released a full movie online. Boy Who Never Slept tells the story of a stagnant insomniac writer who meets a beautiful teenage girl online and falls into an "unlikely love story wrapped in hard reality" and with some sex. As Youtube only allow a maximum of 10 minutes per clip Rothman distributed it in 20 pieces. Took me a while to dig it out but here is the first piece, you can get the rest by searching Solomon Rothman on YouTube:



According to Rothman his hopes are that the new project of Jathia’s Wager "will fully explore the concept of open, collaborative filmmaking and inspire people to create a true open-source filmmaking community." We sure hope so too. It is not yet clear how "fully" it will really be at the end as it seems to be quite a new concept with many edges still remain unsolved. Yet, I think Rothman already deserves my applause for helping us take the first steps into... mmm... how shall we call that? Open Sources Social Movie Making? OSSMM?

Jathia's Wager is not the first collaborative open source movie. A Swarm of Angels, by Steve O'Hear, was recently announced to be moving into its next phase, which "should see the community grow to 5,000 paying members" from just under a thousand in June this year. This interesting article on linux.com titled Can open source methodology make a movie? claims the folks behind The Digital Tipping Point (DTP) are betting it can.

Main Jathia’s Wager page
First Jathia's Wager draft
Official press release
Forums

Tuesday, October 9, 2007

gPhone goes for advertising and Linux



Continuing months of speculations, rumors and global buzz, more details of Google's secret plan to dominate the mobile phone industry have been revealed by The New York Times yesterday. While Microsoft charges mobile phone companies a licensing fee for their Windows Mobile system, Google goes for advertising. If this is true, and the NY Times is not usually easy to manipulate, this might indeed be the large scale Google plan to rival Microsoft's Windows Mobile and redefine the mobile media world.

The most significant aspect of gPhone is that, as opposed to Apple's iPhone and countless of other products using the currently in lead mobile operating systems, it not likely to be another "what a bummer" proprietary, closed environment, mobile device. Even though nothing has been official confirmed by Google it is pretty clear that Google has developed their mobile OS based on Linux kernel for the operating system. As of last talks with folks at Google, the gPhone's user interface is still being finalized and the phone reference design will be open source, using the Apache license. This reference design will be an unlocked, neutral environment.

Dozens of references

Earlier this summer reports from India stated Google is "currently in talks with India's first and third largest telecommunications companies, Bharti Airtel and Vodafone Essar about the Google phone." It is also believed to be in talks with some Indian companies to offer "data, content and platforms including Instant Messaging (IM) and Search functions".

The buzz around gPhone gains interest for its own making some of us wonder how much of it is planned by Google and how much is out of control. Dozens of references to the gPhone project in both online and traditional media channels collected by Search expert Danny Sullivan of SearchEnglineLand are just a very partial list. Google offer 2,820,000 results for gPhone at their major search and 193 entries in the past month within their news search section. By now Google has refused to confirm any plans for the GPhone.

Friday, October 5, 2007

Newseum: 250,000-square-foot museum of American news



Two days ago, on October 3, 2007, more than 200 American newspaper editors from around the nation put the Newseum’s most ambitious interactive exhibits and films to the test during a behind-the-scenes preview. Yet, for pretty obvious reasons American media giants seem to have liked this venture even priorly to this extraordinary effort. Costing $435 million by now NY Times wrote "it may be one of the world’s most expensive museums now under construction" and "certainly among the most prominent, perched on the last buildable site on the presidential inaugural parade route between the Capitol and the White House".



Newseum is a 250,000-square-foot museum of American news "blending the High-Tech with historical" currently under construction at the intersection of Pennsylvania Avenue and Sixth Street, N.W., Washington, D.C. Featuring seven levels of galleries, theaters, retail spaces and visitor services, Newseum will soon allow visitors to experience how and why news is made. "The visitor will come away with a better understanding of news and the important role it plays in all of our lives," says Newseum Executive Director and Senior Vice President Joe Urschel, promising it will be "educational, inspirational and a whole lot of fun."



The folks from Newseum haven’t set an exact opening date yet, but they claim it will be up sometime during 2008. In the meantime they have a fantastic website up at newseum.org. Amongst others news related stuff this website offers a great opportunity to get a close look at daily newspaper front pages in their original, unedited form from 52 states.

http://www.newseum.org

Saturday, August 18, 2007

Skype protocol has been cracked



The proprietary protocol used by Skype for its voip services has been cracked by Chinese programmers, voip startup Vozin Communications co-founder Charlie Paglee reports on voipwiki.com.

Paglee says on July 12, 2006 - more than a year ago(!) - he received a Skype call from a friend at a company in China telling him he was not using Skype to make the call (screenshot above) claiming "his company has successfully reverse engineered the Skype protocol". The friend was after testing the new software with another end user in the United States to see how it worked between physically distant IP addresses.

According to Paglee the Chinees programmers reverse engineered a protocol that was not protected by patent. According to Chinese company CEO, their software will not support Skype’s Super Node technology... digg that :)

 skype

Saturday, August 11, 2007

Free 3-column blogger templates



I've been looking for a decent blogger templates resource for some time now. I simply had to get myself out of this 2-column prison almost every template for the this new Google blogger had. For some reason I didn't came up on Thrbrtemplates on blogspot.com until this morning. I guess I was just not enough into it but now I did so here it is. I used the minima-blue-3col-w960 XML template with a few minor adjustments.

A few Blogger Themes and Templates can be found in the left sidebar. You can grab these templates and install them on your blog through your edit html panel. All templates, other than the one used for the WorkShop design, css and markup, are provided to "use and abuse, beautify and mutilate". There aren't any Terms of Use on this site though it mentions it "would be nice" if you keep their template header information 'as is'.

I also kept this screenshot of the 2-column one (below). Hashem Ykom Dama...

Wednesday, August 1, 2007

My History of Sudoku (数独, sūdoku)



Today I discovered my article The history of Sudoku, written and published mid August 2005, is honored as the fifth on Wikipedia's Sudoku article reference list ('Galanti, Gil. The History of Sudoku. Retrieved on 2006-10-06'). It means I'll have to put some more work into it keeping it updated, but at the same time I should say this is an online form of poetic justice!

Being totally fascinated by the emerging of Wikipedia in those days, and having done a comprehensive research about the subject, I was trying to contribute some of my findings to this article. Yet, I quickly found out that Sudoku has already became "too popular" and the people editing this article had to cope with millions of "contributions" by commercially interested elements. Thus, everything I posted there, no matter how short, interesting or new, was simply gone with the wind after less than 24 hours. I guess thats one of the bummer parts of being a famous puzzle :)

I took the opportunity and got myself updated with some new stuff published in the Wikipedia article. For example, I think Howard Garns - now claimed to be the person who actually made the first Sudokus in 1979 (published by Dell Magazines under the name "Number Place") is new. I need to update my article.

The official Wikipedia Sudoku blurb is now:
Sudoku (数独, sūdoku) is a logic-based number placement puzzle. The objective is to fill a 9x9 grid so that each column, each row, and each of the nine 3x3 boxes (also called blocks or regions) contains the digits from 1 to 9. The puzzle setter provides a partially completed grid.

Completed Sudoku puzzles are a type of Latin square, with an additional constraint on the contents of individual regions. Leonhard Euler is sometimes incorrectly cited as the source of the puzzle, based on his work with Latin squares.

The modern puzzle was invented by an American, Howard Garns, in 1979 and published by Dell Magazines under the name "Number Place".It became popular in Japan in 1986, after it was published by Nikoli and given the name Sudoku, meaning single number. [3] It became an international hit in 2005.

Sunday, July 8, 2007

Microsoft(R) Firefox | We've Made it Better

Just stumbled this "amazingly going all the way to make its point" site with the strange eyecatching domain name of msfirefox.com and could not believe my own eyes. I found myself clicking my way from the About page to the Download looking to see what is going actually on here. Then I had to keep my mouth shut with my palm to avoid my laughter moos from waking everyone at the house. Following is some text from this site about page. Don't miss the rest of it! There is even a Press section...

We provide tools for developing Microsoft standards content

  • Microsoft offers the best implementation of its web standards. Period.
  • By acquiring competitors left, right and center, we offer to to roll a plethora of core technologies into one - removing unnecessary compatibility issues and risks.
  • We utilize scare tactics such as filing lawsuits against companies who we deem as second rate or are providing low-key products to our more deserving users. Such techniques has effectively stabilized core security kernels within technologies such as Microsoft Windows.
We are a slightly open source community

  • We continue to be a leader and partner in slightly open source development, providing low cost*and alternative choices for technology. With millions of users already, we are one of the world's largest distributors of slightly open source software.
  • Our software development processes all take place in the public eye*. We have nothing to hide.
* Official US Civil Antitrust Complaint required

Monday, June 11, 2007

Open Source Alternative: commercial vs opensource software

Providing easy access to high quality open source alternatives to well-known commercial products, Open Source Alternative allows you to browse through the software categories and compare pros and cons of both commercial products as well as open source software. Each category contains a list of opensource software references. On the side one can see the most popular commercial and opensource tools in this category. For example, the boxes below shows most popular for Internet & Networking.

Commercial
MSN Messenger
Citrix Presentation Server
Skype
OpenView Network Node Manager

Open Source
SeaMonkey
Pandora
Pidgin
Zenoss

The site also offer a very nice explanation for the reasons to use opensource software:

"Besides the fact that open source is always available for free, it is a transparent application, in that you are invited exclusively behind the scenes to view all source code and thereby to suggest improvements to the product. Furthermore, every product is covered by a large dedicated network, or community, who is more than willing to answer any questions, you may have."