RT @emblebi: A new @sangerinstitute project is exploring how researchers share results from genome studies. Take the questionnaire: http://bit.ly/xw8Y0k
Tuesday, January 31, 2012
[Samtools-help] Picard release 1.61
Picard release 1.61
30 January 2012
- PicardException used to extend SAMException, which extends RuntimeException. Now PicardException extends RuntimeException directly. If you have code that catches SAMException, you may want to add a catch clause for PicardException if you use the net.sf.picard classes. If you only use classes in net.sf.samtools, you should never see PicardException thrown.
- IlluminaDataProviderFactory.java: Ensure position data type is in set of data types in ctors rather than in makeDataProvider(), in order to avoid ConcurrentModificationException.
-Alec
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Saturday, January 28, 2012
galaxy-user] January 27, 2012 Galaxy Distribution & News Brief
---------- Forwarded message ----------
From: Jennifer Jackson
Date: Saturday, 28 January 2012
Subject: [galaxy-user] January 27, 2012 Galaxy Distribution & News Brief
January 27, 2012 Galaxy Distribution & News Brief
Complete News Brief
* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_27
Highlights:
* Important metadata and Python 2.5 support corrections
* SAMtools upgraded for version 0.1.18. Mpileup added.
* Dynamic filtering, easy color options, and quicker
indexing enhance Trackster
* Set up your Galaxy instance to run cluster jobs as
the real user, not the Galaxy owner
* Improvements to metadata handling and searching in
the Tool Shed
* Improved solutions for schema access, jobs management,
& workflow imports and inputs.
* New datatypes (Eland, XML), multiple tool enhancements,
and bug fixes.
Get Galaxy!
* http://getgalaxy.org
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 26920e20157f
Read the release announcement and see the prior release history
* http://wiki.g2.bx.psu.edu/DevNewsBriefs/
Need help with a local instance?
Search with our custom google tools!
* http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching
And consider subscribing to the galaxy-dev mailing list!
* http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing
--
Jennifer Jackson
Galaxy Team
http://usegalaxy.org
http://galaxyproject.org
http://galaxyproject.org/wiki/Support
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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Changes to Google Privacy Policy and Terms of Service
hmmm unsure if this is for better or worse
---------- Forwarded message ----------
From: Google
Date: Saturday, 28 January 2012
Subject: Changes to Google Privacy Policy and Terms of Service
Is this email not displaying properly?
View it in your browser.
Dear Google user,
We're getting rid of over 60 different privacy policies across Google and replacing them with one that's a lot shorter and easier to read. Our new policy covers multiple products and features, reflecting our desire to create one beautifully simple and intuitive experience across Google.
We believe that this stuff matters so please take a few minutes to read our updated Privacy Policy and Terms of Service at http://www.google.com/policies. These changes will take effect on 1 March, 2012.
One policy, one Google experience
________________________________
Easy to work across Google
Our new policy reflects a single product experience that does what you need, when you want it to. Whether you're reading an email that reminds you to schedule a family get-together or finding a favourite video that you want to share, we want to ensure that you can move across Gmail, Calendar, Search, YouTube or whatever your life calls for, with ease.
Tailored for you
If you're signed in to Google, we can do things like suggest search queries – or tailor your search results – based on the interests that you've expressed in Google+, Gmail and YouTube. We'll better understand which version of Pink or Jaguar you're searching for and get you those results faster.
Easy to share and collaborate
When you post or create a document online, you often want others to see and contribute. By remembering the contact information of the people you want to share with, we make it easy for you to share in any Google product or service with minimal clicks and errors.
________________________________
Protecting your privacy hasn't changed
Our goal is to provide you with as much transparency and choice as possible through products like Google Dashboard and Ad Preferences Manager, alongside other tools. Our privacy principles remain unchanged. And we'll never sell your personal information or share it without your permission (other than rare circumstances like valid legal requests).
Have questions?
We have answers.
Visit our FAQ at http://www.google.com/policies/faq to read more about the changes. (We reckoned our users might have a question or twenty-two.)
________________________________
Notice of Change
1 March, 2012 is when the new Privacy Policy and Terms will come into effect. If you choose to keep using Google once the change occurs, you will be doing so under the new Privacy Policy and Terms of Service.
Please do not reply to this email. Mail sent to this address cannot be answered. Also, never enter your Google Account password after following a link in an email or chat to an untrusted site. Instead, go directly to the site, such as mail.google.com or www.google.com/accounts. Google will never email you to ask for your password or other sensitive information.
---------- Forwarded message ----------
From: Google
Date: Saturday, 28 January 2012
Subject: Changes to Google Privacy Policy and Terms of Service
Is this email not displaying properly?
View it in your browser.
Dear Google user,
We're getting rid of over 60 different privacy policies across Google and replacing them with one that's a lot shorter and easier to read. Our new policy covers multiple products and features, reflecting our desire to create one beautifully simple and intuitive experience across Google.
We believe that this stuff matters so please take a few minutes to read our updated Privacy Policy and Terms of Service at http://www.google.com/policies. These changes will take effect on 1 March, 2012.
One policy, one Google experience
________________________________
Easy to work across Google
Our new policy reflects a single product experience that does what you need, when you want it to. Whether you're reading an email that reminds you to schedule a family get-together or finding a favourite video that you want to share, we want to ensure that you can move across Gmail, Calendar, Search, YouTube or whatever your life calls for, with ease.
Tailored for you
If you're signed in to Google, we can do things like suggest search queries – or tailor your search results – based on the interests that you've expressed in Google+, Gmail and YouTube. We'll better understand which version of Pink or Jaguar you're searching for and get you those results faster.
Easy to share and collaborate
When you post or create a document online, you often want others to see and contribute. By remembering the contact information of the people you want to share with, we make it easy for you to share in any Google product or service with minimal clicks and errors.
________________________________
Protecting your privacy hasn't changed
Our goal is to provide you with as much transparency and choice as possible through products like Google Dashboard and Ad Preferences Manager, alongside other tools. Our privacy principles remain unchanged. And we'll never sell your personal information or share it without your permission (other than rare circumstances like valid legal requests).
Have questions?
We have answers.
Visit our FAQ at http://www.google.com/policies/faq to read more about the changes. (We reckoned our users might have a question or twenty-two.)
________________________________
Notice of Change
1 March, 2012 is when the new Privacy Policy and Terms will come into effect. If you choose to keep using Google once the change occurs, you will be doing so under the new Privacy Policy and Terms of Service.
Please do not reply to this email. Mail sent to this address cannot be answered. Also, never enter your Google Account password after following a link in an email or chat to an untrusted site. Instead, go directly to the site, such as mail.google.com or www.google.com/accounts. Google will never email you to ask for your password or other sensitive information.
Friday, January 27, 2012
Manuel's Personal Exome Now Publicly Released | Manuel Corpas' Blog
After 5 months of having performed the sequencing of my personal exome, I now make it available to the community for public use. I release it under a CC BY-SA 3.0 license, giving you permission to use this data in any way, as long as it provides attribution to the source and it is shared under a similar license.
http://manuelcorpas.com/2012/01/23/my-personal-exome-now-publicly-released/
Thursday, January 26, 2012
Roche in $5.7 billion bid for Illumina
Wow ... Things are going to be interesting now ....
ZURICH/LONDON (Reuters) -Swiss drugmaker Roche Holding AG (ROG.VX) has offered $5.7 billion in cash in a hostile bid to take over Illumina Inc (ILMN.O), and investors are already betting that the U.S. gene sequencing company will command a significantly higher price.
http://mobile.reuters.com/article/innovationNews/idUSTRE80O0FR20120125?irpc=932
Cheers
Kevin
Sent from an Android
Tuesday, January 24, 2012
Why we need the Assemblathon - The Assemblathon
Why we need the Assemblathon - The Assemblathon
excerpted
If you want the best genome assembly possible, you may have to accept some trade-offs. The assemblers that may perform well in one area may not perform as well in other areas. Everybody wants to be told 'genome assembler X will give you the best assembly' but at the moment it doesn't seem fair to make such bold assertions. What we did find out from Assemblathon 1 was that a number of genome assemblers performed admirably across many, but not all, of the different metrics. For example, the assembler that did the best job at increasing coverage (the amount of the known genome present in the assembly), ranked 9th when considering the number of substitution errors present in the assembly. Conversely, the assembler that did the best job at minimizing substitution errors ranked 8th in terms of coverage. You pays your money and you takes your choice. We should mention, however, that these two assemblers (SOAPdenovo and SGA), along with ALLPATHS were consistently ranked among the best assemblers for the vast majority of metrics and were the three best overall assemblers in Assemblathon 1.
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