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Old News*****NEWS January 26th, 2006 Slowly attempting to revamp website, make it more current, add more interesting content *****NEWS January 6th, 2006 ORegAnno manuscript now available through advance access here *****NEWS December 5th, 2005 I have been working on a project called ORegAnno (Open Regulatory Annotation) with Obi Griffith to support some of our research ambitions. It recently got accepted (with minor revisions) for publication in the "Bioinformatics" journal! Check it out at ORegAnno: Open Regulatory Annotation. *****NEWS November 4th, 2005 Awarded the 2005 Lloyd Skarsgard Research Excellence Prize at the BC Cancer Agency Annual Conference!!! *****NEWS July 21st, 2005 Chinook paper published in Nature Methods. Read it at http://www.nature.com/nmeth/journal/v2/n8/full/nmeth0805-563.html. If you do not have an account to Nature Methods, pdfs can be requested directly from me. *****NEWS July 21st, 2005 I have been away since I got married July 2nd, 2005! It was a perfect day and we had an awesome honeymoon in Maui.
*****NEWS May 24th, 2005 A new version of Chinook v1.2.2 has been released. This solves a compatibility problem with the newer version of EnsEMBL. *****NEWS April 9th, 2005 A new version of Chinook has been released. This version includes bug fixes and support for protein data *****NEWS April 9th, 2005 The Chinook Online web application has been released from the Chinook homepage, try it there now *****NEWS April 1st, 2005 New projects in development and new features to existing projects will be announced/released soon. *****NEWS Feb 23rd, 2005 At the International Workshop on Encoding Information in DNA located in Okinawa, Japan. For pictures, click here! Check back frequently for more pictures throughout the week *****NEWS Feb 8th, 2005
Checkout my HUGE air at Big White (courtesy of Ben Good)
*****NEWS Feb 4th, 2005 Checkout this document/example of Grid Computing using Chinook *****NEWS Jan 28th, 2005 Chinook is now permanently licensed under the LGPL (Lesser GNU Public License). It is therefore also OSI-certified. (Open Source in the strictest sense). Disregard all mention to the Creative Common's license; however it would be nice if you still attributed us.
*****NEWS Jan 28th, 2005 Chinook 1.1 released. This large release adds the configure service executable to the Chinook package which allows for wizard-facilitated entry of new applications. This addition makes it even easier to provide new state-of-the-art algorithms from your computer by translating your application entry into a Java Web Service (or exporting it over RMI). See screenshots below. Future plans for this feature are to allow the the remote configuration of Chinook servers and applications using SSL.  
*****NEWS Jan 21st, 2005 Chinook 1.0.3 released, service release to improve flexibility and stability of network. *****NEWS Jan 12th, 2005 Read my lastest blog called "To Google or Not to Google (Yourself)". Sort of a high-tech expose on how self-searching can be used to punish evil-doers. *****NEWS Jan 12th, 2005 Sonata Arctica is coming to Vancouver!!! Get ready for hardcore metal harmonique from Finland. Tix on sale tomorrow.
*****NEWS Jan 9th, 2005 Chinook installers have been put on the install page using Install4J demo version. Try out this new convenient way of installing and running Chinook. *****NEWS Jan 6th, 2005 It is the International Year of the Physicist!!! As you may be aware :), on CBC radio, during the holidays, they had a limerick contest honoring this important year. My folks and I got in on this action and had limericks played on the radio. Here are my best physics limericks and the ones which got played. My CBC-aired entry was: A student at U.B.C. My mom's CBC-aired entry (may not be quite accurate from my memory) was: The soft-hearted Madame Curie My second, more morbid entry was: A physicist, Bob Oppenheimer Ones that never got entered, since they were thought of after: A physicist going to U.Vic. A student at S.F.U. Alas, we did not win anything but had a good time :) *****NEWS Dec 20th, 2004 Zhiping Weng's lab at Boston University has become the first non-Vancouver location to use Chinook. Special thanks to Ulas Karaoz who set-up this up and really made it all happen. Zhiping's lab is offering two of their tools as services over the Chinook network: Cluster-buster and Clover. This is a significant accomplishment for Chinook as we were able to start it in Boston and find the service less than 10 seconds later here in Vancouver - which means the initial advertisement propagation speed is really quick. Coast-to-coast yeah! See what servers and tools are being offered by clicking here.
*****NEWS Dec 9th, 2004 Real-time service status is available for Chinook. See what servers and tools are being offered by clicking here.
*****NEWS Dec 6th, 2004  Download Chinook 1.0
*****NEWS Nov 29th, 2004 Chinook Update: From the Chinook web-site linked to here. All user documentation, talks, and developer's guides have been put on the site. All documentation and slides are licenced under Creative Common's Attribution license.
*****NEWS Nov 18th, 2004 Chinook Update: A small revision to database configuration is being wrapped up. This will allow support for various non-sequence databases. The current stage of this revision is to finish the required GUI elements, then update the Perl interface. The Perl interface needs a few days of work since it has lapsed into a bit of disrepair as of late. The goals before the next release are to:
*****NEWS Nov 9th, 2004 Chinook Update: Chinook (v1.0) can be run from web start. Try out peer-to-peer bioinformatics now! If there are any problems, feel free to e-mail chinook@bcgsc.bc.ca Other Update: For a good read (at least 7/10ths of it so far) check out Neal Stephenson's Cryptonomicon. Or for that matter, Margaret Atwood's Oryx and Crake. *****NEWS Oct 27th, 2004 Chinook Update: Chinook nodes are running at the CMMT and at the GSC. We have also been giving out the source. Unfortunately, one or two wrap up things to do before a general release. But still, ask for it, check it out. We had a successful demo at the CMMT today of Chinook in action. I'm still trying to clean-up the bioperl interface and ensure that the code will maintain its compatibility across versions. Shouldn't be too much work... Other Update: Planning to open a regulation analysis section to the website to start releasing software I have been developing for gene regulation prediction. It is called the "Oh yeah, I have to do a thesis" Section. *****NOTICE: You may (or likely may not) be wondering, why the inactivity during this period of time. I apologize. *****NEWS Jul 5th, 2004 Steve Jones' GeneViews resource links HUGO human gene names to Sockeye. Visit it here
*****NEWS Jul 5th, 2004 Focussed upgrade on Chinook is wrapping up. This will allow easier support for more complicated algorithms like Orca and Blast. Furthermore, expansion of Chinook into more complicated data types (other than sequence). And a new and improved GUI with the ability to store jobs for viewing later, estimates on time to complete of processing jobs, and server/version information. Below is a sneak preview of the main panel of the new GUI (more screenshots of data entry to be released later this week)
 
*****NEWS May 30th, 2004 Philippe Online has put out the memorable May long-weekend photos for Tofino 2004. Check them out here! Also, hear Philippe sing all your favorites by checking out his playing schedule here!
 
*****NEWS May 28th, 2004 Went and saw the movie Super Size Me. Absolutely fascinating/disturbing. Very funny. Even more interesting are the weblogs people have had about it (everyone has an opinion). Check it out! *****NEWS May 28th, 2004 Chinook made perl-ready. The beta version of Chinook has been integrated into the Bioperl framework. This enables users of Chinook to find jobs and dispatch them via their perl scripts. Future revisions will seamlessly integrate the Bio::Seq object with the Sequence parameters required for Chinook. This revision is designed to improve the scope of applications that use Chinook for their service-handling requirements. *****NEWS May 20th, 2004
*****NEWS May 19th, 2004 Chinook development mentioned in the May 2004 Genome Technology Magazine here. 
*****NEWS May 19th, 2004
*****NEWS May 3rd, 2004 Sockeye paper published in Genome Research. Visit it here! *****NEWS Apr 28th, 2004 Chinook was awarded the 2004 BCNet "Best Application Award" at the 4th Annual BCNet 2004 Advanced Networks Conference. My colleagues at the GSC and myself are extremely honored to be receiving this award from BCNet and the award sponsors, in no particular order, fSONA, BC Ministry of Management Services, CANARIE, Industry Canada, Creo, and Reboot Communications Ltd. *****NEWS Apr 4st, 2004 Welcome to the new site. Frames are gone, CSS in use, and information laid out similar to main CMSGSC site. *****NEWS Apr 1st, 2004 Chinook spotlighted on the Canadian Bioinformatics Helpdesk newsletter. You can also check out the Sockeye spotlight from the Feb. 4th issue here. *****NEWS Mar 30th, 2004 smweb.bcgsc.bc.ca sponsors google web-site advertising. Currently, this is displayed above from the main page. Future website plans include creating a frameless upgrade on the existing site because according to the webmaster, "frames are old-school". *****NEWS Mar 29th, 2004 The GSC's "Everybody in the lab gettin tipsy" team competed in the 2004 UBC Storm the Wall. Events began precariously as we tried to get Perseus registered at the last minute. Accepting an automatic DQ for our smaller than regulation registrated number of team members, EITLGT competed with a ferocity that had never been seen before at this event. I started us off in the pool for a 225 metre swim coming in last in my heat by a hair. Angelique took us to the 450 metre sprint gaining ground on our start but not passing anybody. Monica drove EITLGT further with her 2.8km bicycle sprint. Obi brought us back to the wall after his 1km endurance run. It was here that the entire EITLGT team met up with Perseus and scaled the 12ft wall. Obi and I quickly got Obi over. Angelique and I followed by getting Perseus over where they supported getting myself, Angelique, and Monica over the wall in outstanding time. Unfortunately, we came last in our heat but the lessons learnt and the hardships endured will have changed us for the rest of our lives. *****NEWS Mar 27th, 2004 The Michael Smith Foundation for Health Research MSFHR named their 2004 Trainee Awards. I received a Senior Graduate Scholarship!!! 
*****NEWS Mar 27th, 2004 Chinook to win BCNet Coolest Application Award at BCNet's Advanced Networks Conference BCNet Advanced Networks Conference *****NEWS Mar 11th, 2004 Java APIs for Bioinformatics at www.onjava.com. Or directly, here. *****NEWS Mar 8th, 2004 Initial image of Sockeye in the CAVE at the University of Calgary. For more info on the CAVE, check out this U of C news release here. 
*****NEWS Mar 3rd, 2004 Check out my Java, Bioinformatics weblogs at www.java.net. Or directly, here. *****NEWS Feb 27th, 2004 Check out the Chinook spotlight on jxta.org. JXTA is the P2P API that Chinook uses to advertise bioinformatics APIs. Alternately, you can view the spotlight directly by clicking here. 
*****NEWS Feb 25th, 2004 Do you want to have the skills to build advanced bioinformatics tools? Do you constantly wonder how you can make your bioinformatics applications better? More maintainable? More accessible? If so, sign up for the latest Canadian Bioinformatics Workshop, "Developing the Tools" and explore a bioinformatics world without limitations. Start your adventure here *****NEWS Feb 25th, 2004 Sockeye mentioned on homepage of the Lagan website. Sockeye allows users to generate alignments using Lagan through the Chinook architecture. Visit Lagan here 
*****NEWS Feb 18th, 2004 Site has been reformatted and chinook web start client has been updated. *****NEWS Feb 17th, 2004 CHECK IT OUT. Human-Mouse-Rat data service page online. This page hosts tools to obtain WGA data from Berkeley and UCSC datasets. WGA Data service *****WEBLOG Feb 10th, 2004 Java vs Perl for Bioinformatics
*****NEWS Jan 27th, 2004 Version 1.1 of Sockeye Comparative Genome Browser released. Mentioned on Wormbase. Allows users to switch between normal and development P2P version of Chinook. 
*****NEWS Jan 17th, 2004 Sockeye Comparative Genome Browser release 1.1 soon. Will not have P2P as default yet. This can be turned on from the XML configuration file (user_config.xml). Working to increase content on external Sockeye website. Chinook has been made Tomcat/Axis web services ready and deployable via Ant. Will add option to target known servers. Design for auto-submission completed. It is basically going to be two directories: one which has the specs to complete certain services and another that is polled and completes jobs that are put into the directory. This will be run via a special Chinook client executable since it is a non-standard mode of operation designed to support more background pipelining capabilities. The Chinook Client will no longer try to become a rendezvous by default. Saves ~15-30 seconds on start-up. *****NEWS Jan 16th, 2004 New document on adding / editing features added to Sockeye Comparative Genome Browser website *****NEWS Jan 10th, 2004 CMMT made Chinook capable. New features to aid in auto-submission planned to be added. *****NEWS Dec 17th, 2003 Passed comprehensives!!! *****NEWS Dec 4th, 2003 Studying for comprehensives until Dec. 16th, 2003. All other work postponed. Requests snapshots of source directly. *****NEWS November 25th, 2003 Chinook is in Sockeye!!! And that conjures a confusing image if interpretted literally. We have set-up 8 services on island. Why is there no source yet. Well, I'm working on it... :) Soon. The bug list is a couple of dozen (but all minor) and my teammates are more eager to start using Chinook themselves then getting it accessible to all. But look forward to a CMSGSC and a CMMT Chinook server peer soon. I promise that the source will be available to all and the license has been decided on as GPL. Below is the Chinook splash screen in Sockeye. 
*****NEWS October 29th, 2003 Chinook peer to peer (P2P) source is not yet available. Licensing issues must be taken care of and appropriate commenting is currently being included. Check back later this week or early next week for download instructions *****NEWS October 27th, 2003 Chinook source is on bioinformatics.org. A web start application and documentation have been uploaded. *****NEWS October 14th, 2003 Sockeye on November LJ Cover 
*****NEWS October 3rd, 2003 Probably the only time that I will post twice in a day, look for SOCKEYE on the cover of the November Linux Journal *****NEWS October 3rd, 2003 Welcome to the new site. Tried to take care of poorly-formatted original site. I'll try to get some Java stuff on here soon. I'm also thinking about an applet that monitors Chinook activity - how cool would that be. Cheers. | |||||||||||||||||||||||||||||||||||||
A fellow Ph.D. graduate student
in the gene regulation group at the GSC, and my cubicle buddy, Obi
Griffith, was announced by Maclean's magazine as one of the
Best and the Brightest. Congratulations dude!!! 
Chinook development highlighted
in focus on the | top | Canada's Michael Smith Genome Sciences Centre | Genetics Graduate Program (UBC) | Want bioinformatics training??? | Vancouver Bioinformatics Users Group | |
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(c) 2004 Stephen Montgomery, Canada's Michael Smith Genome Sciences Centre |
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