My Weblog on Bioinformatics, Genome Science, Next Generation Sequencing

FAQ Admin/Data Libraries/Uploading Library Files local instance - Galaxy Wiki

2012-02-14T17:11:00.001+08:00

This is a FAQ that's best answered in the Wiki page
the most intuitive is to use the web GUI to upload but this creates unnecessary overhead and slowdown when you can point to the files

Options for Uploading Files from the Admin Perspective

There are currently four options available to a Galaxy admin user for uploading files to a data library. Some of these same options are available to all regular users that have been granted permission to add items to a Data Library or folder, but this section describes the features from the Galaxy admin perspective which is accessed by clicking on the "Admin" link in the top Galaxy menu bar.
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

Get to Know Btrfs | Linux.com

2012-02-13T16:07:00.000+08:00

https://www.linux.com/learn/tutorials/533112-weekend-project-get-to-know-btrfs

As expected, Storage Spaces will indeed be a feature of both desktop and server editions of the operating system.
If the feature does indeed ship in desktop Windows, it will overnight obsolete a range of SOHO-oriented storage systems; products like Drobo and ReadyNAS will find it hard to survive in a Windows 8 world.

Btrfs Features

RAID 0, 1, 10
COW
Incremental backup
Online defrag
gzip and LZO compression
Space-efficient packing of small files
Dynamic inode allocation
Checksums on data and metadata
Shrink and grow storage volumes
Extents
Snapshots
16 EiB maximum file size

Planned features include RAID 5 and 6, deduplication, and a ready-for-primetime filesystem checker, btrfsck. You can try out btrfsck now because it is included in btrfsprogs. (Which of course Debian/Ubuntu/Mint etc. changes to btrfs-tools, and Fedora calls it btrfs-progs.) But it is not ready for production systems yet.
Putting the finishing touches on btrfsck is the last big step before Oracle makes it the default filesystem in their next Unbreakable Linux release. Fedora 16 Linux was supposed to default to Btrfs, but now they're aiming for Fedora 17 in May 2012.

also see https://btrfs.wiki.kernel.org/

Windows 8 Storage Spaces detailed: pooling redundant disk space for all

2012-02-13T16:01:00.000+08:00

This will definitely change mainstream consumer ideas on backup and data storage .. maybe it will ripple down to labs who currently do not backup their data ..

Windows 8 Storage Spaces detailed: pooling redundant disk space for all
http://arstechnica.com/microsoft/news/2012/01/windows-8-storage-spaces-detailed-pooling-redundant-disk-space-for-all.ars

Unlike RAID systems of old, but in common with other modern storage technologies such as Solaris' ZFS and Linux's btrfs, pools can use disks of different interface technologies—USB, SATA, Serial Attached SCSI—and different, mismatched sizes. New disks can be added to a pool at any time. Pools can also include one or more hot spares: drives allocated to a pool but kept in standby until another disk in the pool fails, at which point they spring into life.

As expected, Storage Spaces will indeed be a feature of both desktop and server editions of the operating system.
If the feature does indeed ship in desktop Windows, it will overnight obsolete a range of SOHO-oriented storage systems; products like Drobo and ReadyNAS will find it hard to survive in a Windows 8 world.

Article: Running Python and R inside Emacs

2012-02-10T10:15:00.001+08:00

Running Python and R inside Emacs
http://www.johndcook.com/blog/2012/02/09/python-org-mode/

Unix join on more than two files - Stack Overflow

2012-02-09T23:39:00.001+08:00

http://stackoverflow.com/questions/9212893/unix-join-on-more-than-two-files

This has to be useful someday ...

ea-utils - FASTQ processing utilities - Google Project Hosting

2012-02-09T15:42:00.000+08:00

didn't cc Rick cos he's away, heh share with him later ..

http://code.google.com/p/ea-utils/

Suite of processing tools for sequencing output. Barcode demultiplexing, adapter trimming, etc.

Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

Overview:

fastq-mcf

Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering.

fastq-multx

Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not.

fastq-join

Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same "squared distance for anchored alignment" as other tools.

Other Stuff:

sam-stats - Basic sam/bam stats. Like other tools, but produces what I want to look at, in a format suitable for passing to other programs. (Click for source)

fastq-stats - Basic fastq stats. Counts duplicates. Option for per-cycle stats, or not (irrelevant for many sequencers). (Click for source)

determine-phred - Returns the phred scale of the input file. Works with sams, fastq's or pileups and gzipped files.

Chrdex.pm - indexes a delimited file by chromosome start/stop. There are lots of tools for this. This one works pretty well if you're a perl user. It handles overlapping regions reasonably well. It uses RAM comparable to the size of the annotation file.

Sqldex.pm - just like Chrdex.pm, except uses a disk-based btree. Not as fast, but close, and uses very little RAM.

qsh - Runs a bash script file like a "cluster aware makefile"...only processing newer things, die'ing if things go wrong, and sending jobs to a queue manager if they're big. That way you don't have to write makefiles, or wrap things in "qsub" calls for every little program. Not really ready yet.

grun - Fast, lightweight grid queue software. Keeps the job queue on disk at all times. Very fast. Works well by now

gwrap - Bash wrapper shell that downloads all dependencies that are not the local system.... good for EC2 nodes. Linux only. Will use it if we ever go to EC2.

Amazon S3 Lowers Standard Storage Prices

2012-02-07T23:23:00.001+08:00

Dear Amazon S3 Customer,

We are excited to announce that we have reduced the Amazon S3 standard storage prices in all regions. With this price change, all Amazon S3 standard storage customers will see a reduction in their storage costs. For instance, if you store 50 TB of data on average, you'll see a 12% reduction in costs. If you store 500 TB of data on average, you'll see a 13.5% reduction in costs. The price reduction applies to all of your standard storage- both existing storage and all new storage you add. Here is a summary of price changes for the US Standard region:

Old New
First 1TB $0.140 $0.125
Next 49TB $0.125 $0.110
Next 450TB $0.110 $0.095
Next 500TB $0.095 $0.090
Next 4000TB $0.080 $0.080 (no change)
Over 5000TB $0.055 $0.055 (no change)

The new lower prices for all regions can be found on the Amazon S3 Detail Page. New prices are effective February 1st and will be applied to your bill for all storage on or after this date.

We are happy to pass along these savings to you as we continue to innovate and drive down our costs.

Sincerely,
The Amazon S3 Team

We hope you enjoyed receiving this message. If you wish to remove yourself from receiving future product announcements and the monthly AWS Newsletter, please update your communication preferences.

Amazon Web Services LLC is a subsidiary of Amazon.com, Inc. Amazon.com is a registered trademark of Amazon.com, Inc. This message produced and distributed by Amazon Web Services, LLC, 1918 8th Avenue, Seattle, WA 98101.

Google Refine is a power tool for working with messy data sets

2012-02-07T17:52:00.000+08:00

http://google-refine.blogspot.com/

Google Refine is a power tool for working with messy data sets, including cleaning up inconsistencies, transforming them from one format into another, and extending them with new data from external web services or other databases. Version 2.0 introduces a new extensions architecture, a reconciliation framework for linking records to other databases (like Freebase), and a ton of new transformation commands and expressions.

Public Poll: What data storage solutions are you using now?

2012-02-06T14:34:00.002+08:00

BooRoo

Just a public poll created curious as to what systems are out there and what is being used day to day. Results are immediately viewable. Order of choices is randomized.

Which data storage platform are you using?

http://www.bluearc.com/ BlueArc is your Life Sciences Solution0%

http://www.isilon.com/ Isilon scale-out NAS, BIG data is no longer a challenge, it’s an opportunity.0%

http://www.panasas.com/ PANASAS SOLVES BIG DATA PROBLEMS0%

http://www.ddn.com/ DataDirect Networks’ (DDN) Big Data Storage Technology Powers More0%

http://aws.amazon.com/ Store data and build dependable backup solutions using AWS’s highly reliable, inexpensive data storage services.0%

Inhouse solutions using commodity hardware0%

http://www-03.ibm.com/systems/software/gpfs/ IBM GPFS0%

Other: (Please specify)0%

Create an online survey quiz or web poll

[circos] Circos v0.56 released

2012-02-06T12:37:00.001+08:00

---------- Forwarded message ----------
From: "Martin"
Date: Feb 6, 2012 9:56 am
Subject: [circos] Circos v0.56 released

Dear Circos users!

I have made v0.56 available.

http://circos.ca/software/download/

Thank you to everyone who submitted bug reports and patiently waited
for me to respond.

Remember that now tutorials and the core code are kept separate. The
core circos-0.56.tgz archive contains an example directory (example/)
that creates a relatively complex image. Use this to ensure that
everything is working.

Most of the changes are bug fixes. Error handling is improved - many
errors have a gentler format and should be more explanatory.

*** IMPORTANT CHANGES AND REMINDERS ***

1. Import colors/fonts/patterns all at once

Use a single line to add color, font and pattern definitions in
circos.conf:

<<include etc/colors_fonts_patterns.conf>>

instead of

<colors>
<<include etc/colors.conf>>
...

Note that colors.conf now imports brewer.conf automatically.

Please see example/etc/circos.conf for ideas of how to make your
configuration more modular.

2. Make sure you're using etc/housekeeping.conf

A while back, I had centralized system parameters that used to appear
at the bottom of circos.conf into a separate file. For those of you
who still have these parameters in their circos.conf file, please
remove them.

<<include etc/housekeeping.conf>>

instead of

anglestep = 0.5
minslicestep = 10
beziersamples = 40
debug = no
warnings = no
imagemap = no
units_ok = bupr
units_nounit = n

3. Use debug_group

You'll notice that Circos' default debug output contains more text. By
default debugging that falls into the 'summary' category is created. A
complete list of debug categories is listed here

http://mkweb.bcgsc.ca/dev/circos/documentation/tutorials/configuration/debugging/

In particular, the following are very useful

timer - show code timings
io - loading and locating files
textplace - reports whether a text in a text track has been
successfully placed

4. SVG text handling improved

I've revamped how SVG text labels are placed. You'll notice that fonts
now have font family definitions in etc/fonts.conf. This string is
used in the SVG file to specify the font. Once you have the font
installed on your system, labels won't all appear in the SVG app or
viewer default (e.g. Arial) font.

There's still more to do here, but it's getting better.

0.56 CHANGELOG

Parallel ideogram labels are now centered with respect to the
ideogram.

restrict_parameter_names now controls whether parameters are
restricted to a pre-defined list (e.g. color, thickness, etc). If you
have custom parameters (e.g. 'myspecialcode') then set
restrict_parameter_names=no. By default, this is always set to 'yes'.

Added link_orientation for text tracks. When set to "out" links from
text labels face out, rather than in.

Added font names to SVG files via font-family tag.

Removed -verbose. The -v flag now reports version.

Removed dependence on Graphics::ColorObject.

Added error handling framework.

Circos now requires Text::Format

Bug fix to heat map color mapping of last color.

Fixed bug which was causing line links to be drawn with a thickness
half of what was requested.

Fixed bug that prevented parameters made acceptable by the
restrict_parameter_names=no setting from being parsed.

Configuration file location is now guessed if guess_conf_location=yes
(see etc/housekeeping.conf)

Color file cache can now be static (color_cache_static) and dir/file
can be changed (color_cache_{file,dir})

Added 'placed' and 'not_placed' output for labels in text tracks to.
Use -debug_group text to see this.

# create data file of labels that were not placed
circos -conf ... -debug_group text | grep not_placed >
text.notplaced.txt

Parts of the code were made faster (unit checking) through Memoize.

Fixed a bug which prevented links with thickness=1 from being shown
with correct transparency.

Fixed bug in which color errors were produced when PNG file was not
asked for.

Fixed bug in which opacity of links in SVG files was missing in some
cases.

Fixed but which was assigning the wrong color to transparent links in
PNG files in some cases.

Centralized color configuration files colors.conf now includes
brewer.conf - no need to include brewer.conf separately.

Added -paranoid flag to exit on warnings.

Made error messages friendlier. Revamped internal error handling
mechanism.

Added data_path to allow adding to locations where files are searched
for.

Added data/ to prefix path of locations where files are searched for.
Now the default search locations are

{ CWD | CIRCOS_PATH } + { . | .. | ../.. } + { . | etc | data }

--
You received this message because you are subscribed to the Google Groups "Circos" group.

Hive Plots - Linear Layout for Network Visualization - Visually Interpreting Network Structure and Content Made Possible

2012-02-05T19:31:00.001+08:00

http://mkweb.bcgsc.ca/linnet/

Krzywinski M, Birol I, Jones S, Marra M (2011). Hive Plots — Rational Approach to Visualizing Networks. Briefings in Bioinformatics (early access 9 December 2011, doi: 10.1093/bib/bbr069). (download citation)

the hive plot is a perceptually uniform and scalable linear layout visualization for network visual analytics

UNDERSTANDING NETWORK STRUCTURE WITH HIVE PLOTS.

(A) Normalized (top) and absolute (bottom) connectivity of E. coli gene regulatory network and Linux function call network (Yan et al.)

(B) Gene co-regulation networks in neuroblastoma samples.

(D) Syntenic network of three modern crucifer species to ancestral genome.

(E) Layered network correlation matrix. In each cell two layers u,v are depicted with u used to order axes and nodes while links for v are shown.

Hive plots — for the impatient

The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links. Simple and interpretable.

The purpose of the hive plot is to establish a new baseline for visualization of large networks — a method that is both general and tunable and useful as a starting point in visually exploring network structure.

Hive plots give the reader a passing chance to quantitatively understand important aspects of a network's structure. Unlike hairballs, hive plots are excellent at managing the visual complexity arising from large number of edges and exposing both trends and outlier patterns in network structure.

only for networks?

No.

Hive plots can be applied to data structures other than networks. The method requires that your data be mappable onto a set of pairwise relationships. For networks, this pairwise relationship is the edge between two nodes. In other circumstances, it can relate two spatial positions (where the axis corresponds to an object with a physical length scale) or two intervals (two axis segments are related, thereby creating a ratio comparison).

This hive plot provides a visual recipe for assessing the quality of a genomic assembly. An assembly is composed of reads (bottom axis), which are assembled into contigs (right axis). Independently, a reference assembly (left axis) may exist and act as a comparator. Among others, this hive plot answers the following questions

what fraction of reads are unassembled? 20%
what fraction of reads are unaligned to reference? 30%
what fraction of reference has no read coverage? 2%
what fraction of reference has no contig coverage? 15%
what fraction of reference is constructed by contigs < 200kb? 60%
are there contigs > 200kb? no.
what fraction of contigs are unaligned to the reference? 20%
what fraction of the overall assembly is derived from k=27 assembly? 80%

The benefit of this stacked bar plot layout is that the circular layout is both periodic and has visual weight. This approach is similar to a parallel coordinate plot, except here the plot wraps around.

Multiple panels can be combined to display a very large number of ratios. Below are shown 3 x 3 x 3 (27) comparisons, each with 3 x 8 ratios, for a total of 648 ratios. By categorizing each ratio using a spectral color scheme, patterns can be quickly spotted and interpreted. The image below was created for the EMBO Journal 2011 cover contest.

R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data

2012-02-03T02:06:00.001+08:00

http://nar.oxfordjournals.org/content/early/2012/01/28/nar.gks047.long

The rapid expansion in the quantity and quality of RNA-Seq data requires the development of sophisticated high-performance bioinformatics tools capable of rapidly transforming this data into meaningful information that is easily interpretable by biologists. Currently available analysis tools are often not easily installed by the general biologist and most of them lack inherent parallel processing capabilities widely recognized as an essential feature of next-generation bioinformatics tools. We present here a user-friendly and fully automated RNA-Seq analysis pipeline (R-SAP) with built-in multi-threading capability to analyze and quantitate high-throughput RNA-Seq datasets. R-SAP follows a hierarchical decision making procedure to accurately characterize various classes of transcripts and achieves a near linear decrease in data processing time as a result of increased multi-threading. In addition, RNA expression level estimates obtained using R-SAP display high concordance with levels measured by microarrays.

To initiate analyses using R-SAP, the user provides two required inputs for the pipeline: the sequence alignment file and known transcripts’ coordinate file. Currently R-SAP accepts alignment files only in psl format that are generated by mapping RNA-Seq reads to the reference genome using BLAT (Blast like alignment tool) (21) or SSAHA2 (Sequence search and alignment by hashing algorithm) (22). RNA-Seq reads mapping to the genome may result in the alignments scattered across multiple exons separated by introns. We chose psl as the alignment format for the pipeline because the scattered alignments are precisely stitched together and reported as a large single alignment. As a result, for each sequencing read the most likely alignment and corresponding genomic locus can be readily found in the alignment files. Moreover, the psl format preserves the orientation of alignment blocks originating from the contiguous genomic loci enabling their accurate re-mapping to the annotated exons and determination of associated reference structural variants.

R-SAP is also configured to work with two of the currently available transcript assemblers: Cufflinks (23) and Scripture (24). Assembled transcripts can be supplied to R-SAP either in GTF (Gene Transfer Format) or in BED (Browser Extensible Data) format. GTF and BED are default output formats from Cufflinks and Scripture respectively.

Nucl. Acids Res. (2012) doi: 10.1093/nar/gks047 First published online: January 28, 2012

This article is Open Access

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

2012-02-03T02:02:00.000+08:00

http://nar.oxfordjournals.org/content/early/2012/01/28/nar.gks043.long

With the development of next-generation sequencing (NGS) techniques, many software tools have emerged for the discovery of novel microRNAs (miRNAs) and for analyzing the miRNAs expression profiles. An overall evaluation of these diverse software tools is lacking. In this study, we evaluated eight software tools based on their common feature and key algorithms. Three deep-sequencing data sets were collected from different species and used to assess the computational time, sensitivity and accuracy of detecting known miRNAs as well as their capacity for predicting novel miRNAs. Our results provide useful information for researchers to facilitate their selection of the optimal software tools for miRNA analysis depending on their specific requirements, i.e. novel miRNAs discovery or miRNA expression profile analysis of sequencing data sets.

Are we slaves to the scientific publishing industry?

2012-02-03T00:50:00.001+08:00

Found this fascinating analogy in the post http://conservationbytes.com/2012/01/29/knowledge-slavery/

...our slavery to the scientific publishing industry.

And 'slavery' is definitely the most appropriate term here, for how else would you describe a business where the product is produced by others for free¹ (scientific results), is assessed for quality by others for free (reviewing), is commissioned, overviewed and selected by yet others for free (editing), and then sold back to the very same scientists and the rest of the world's consumers at exorbitant prices.

This isn't just a whinge about a specialised and economically irrelevant sector of the economy, we're talking about an industry worth hundreds of billions of dollars annually. In fact, Elsevier (agreed by many to be the leader in the greed-pack – see how some scientists are staging their protest; also here) made US$1.1 billion in 2010!

what are your thoughts? I don't think that making money is necessarily bad, but apparently rich is even a derogatory term now, with rich ppl (oops) preferring to be called high net worth individuals. But when it's larger entities, corporations, it might be easy to mud sling them.
However, I think the author has a point when making the analogy, my 1st shock was discovering that I have to read lengthy copyright info on what I can or cannot do with something that I researched / wrote (see http://www.elsevier.com/wps/find/authorsview.authors/rights )

It's so much easier to understand from a photographer's point of view
http://www.photosecrets.com/photography-law-copyright

"Copyright" is "the right to copy." This right is a legal construct, designed for you — the artist — to support your artistic endeavors. Without copyright, people would be free to use your artistic work
You can negotiate a "license" to copy, and perhaps even get paid in real money. Hopefully this will give you more incentive to create art, and the world will be a better place.

Will People Steal My Work?

Generally no, as publishers live by copyright law and usually have established rates which they gladly pay. A more likely problem is that publishers may not know that you are the copyright owner, which goes back to that "©" symbol and digital watermark.

Hey wait a minute .. "the world will be a better place " hmmm I thought scientists are the ones trying to help the world with advancing human knowledge where our incentive to churn out more scientific results?

hmmm food for thought ..
Post comments!

How do u share ur results from genome studies?

2012-01-31T23:37:00.001+08:00

RT @emblebi: A new @sangerinstitute project is exploring how researchers share results from genome studies. Take the questionnaire: http://bit.ly/xw8Y0k

[Samtools-help] Picard release 1.61

2012-01-31T07:37:00.001+08:00

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

------------------------------------------------------------------------------
_______________________________________________
Samtools-help mailing list
https://lists.sourceforge.net/lists/listinfo/samtools-help

galaxy-user] January 27, 2012 Galaxy Distribution & News Brief

2012-01-28T16:04:00.001+08:00

---------- 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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/

Changes to Google Privacy Policy and Terms of Service

2012-01-28T16:02:00.001+08:00

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.

Manuel's Personal Exome Now Publicly Released | Manuel Corpas' Blog

2012-01-27T17:21:00.001+08:00

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/

Roche in $5.7 billion bid for Illumina

2012-01-26T04:54:00.001+08:00

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

Why we need the Assemblathon - The Assemblathon

2012-01-24T21:49:00.001+08:00

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.

Read it online: http://assemblathon.org/why-we-need-the-assemblathon

Free Science, One Paper at a Time | Wired Science | Wired.com

2012-01-22T01:28:00.001+08:00

http://m.wired.com/wiredscience/2011/05/free-science-one-paper-at-a-time-2/all/1

Part of the answer, strangely, is the very thing at the center of science: the paper. Once science's main conduit, the paper has become its choke point.

It's not just that the paper is slow, though that is a huge problem. A researcher who submits a paper to a traditional journal right now, for instance, won't see the published piece for about a year. She must wait while the paper gets passed around among editors, then goes through rounds of peer review by experts in her field, who might and often do object not just to her methods or data but to her findings and interpretations. Finally, she must wait while it moves through an editing, layout, and publishing pipeline that itself might run anywhere from 2 to 12 weeks.

Yet the paper is not simply slow; it's heavy. Even as increasingly data-rich science has outgrown the paper's ability to deliver and describe all that science has to offer — its deep databases, its often elaborate methods — we've loaded it up needlessly with reputational weight and vital functions other than carrying data.

The paper is meant to be a conduit for the real content and currency of the science: the ideas, methods, data, and findings of the people who do science. But the tremendous publishing and commercial infrastructure built around the academic paper over the last half-century has concentrated so many functions and so much value in the journal that the paper itself, rather than the information in it, has become science's main currency. It is the paper you must buy; the paper you must publish; the paper you must cite; the paper on which not just citations but tenure, reputation, status, and even school rankings are built

SGA uses less memory for de novo assembly

2012-01-21T13:19:00.001+08:00

excerpted from Genomeweb

According to a Genome Research paper describing the method, the secret to the String Graph Assembler's reduced memory footprint is that it uses compressed data structures to "exploit the redundancy" in sequence reads and to "substantially lower the amount of memory required to perform de novo assembly."

SGA relies on an algorithm its developers published in 2010 that constructs an assembly string graph from a so-called “full-text minute-space” index, or FM-index, which enables searching over a compressed representation of a text. Unlike other short-read assemblers that rely on the de Bruijn graph model, which breaks reads up into k-mers, the string graph model “keeps all reads intact and creates a graph from overlaps between reads,” the Sanger team wrote.

his approach makes even more sense now that sequencing instruments like the Pacific Biosciences RS are generating longer reads.

In the paper, Durbin and co-developer Jared Simpson report that SGA successfully assembled 1.2 billion human genome sequence reads using 54 GB of memory. This was compared with SOAPdenovo, which required 118 GB for the same task.

Results from comparisons of SGA with Velvet, ABySS, and SOAPdenovo using a C. elegans dataset showed that its assembled contigs covered 95.9 percent of the reference genome while the other three programs covered 94.5 percent, 95.6 percent, and 94.8 percent respectively.

Furthermore, SGA required only 4.5 gigabytes of memory to assemble the C. elegans dataset compared to 14.1 GB, 23 GB, and 38.8 GB required for ABySS, Velvet, and SOAPdenovo respectively.

SGA is slower that its counterparts, however. SGA took 1,427 CPU hours to complete a human genome assembly, while SOAPdenovo required 479 CPU hours.

"We explicitly trade off a bit longer CPU time for lower memory usage," Simpson, a doctoral student in Durbin's lab, told BioInform. "We feel that fits better into most of the clusters that are available right now."

On the other hand, SGA is parallelizable, so its most compute-intensive activities — error-correcting reads and building the FM-index of corrected reads — can be distributed across a compute cluster to reduce run time, the researchers explain in the paper.

He explained that while de bruijn assemblers like Velvet require a separate processing step after completing the genome assembly, SGA doesn’t and potentially avoids "some of the errors or incomplete analysis" that can occur in the extra processing step.

This reduced error risk plus its lower memory requirement ensures that tools like SGA have a "future," Durbin said.

For their next steps, Durbin and Simpson are adapting SGA to work with longer read data from the Roche 454 sequencer and the Life Technologies Ion Torrent Personal Genome Machine. They are also exploring ways of discovering variants using the program.

The approach could also be used to analyze metagenomic data, the researchers said in the paper.

Read the full article here http://www.genomeweb.com/informatics/sanger-teams-de-novo-assembler-adopts-compressed-approach-reduce-memory-footprin

1427 CPU hours is ALOT more than 479 CPU hours (~ 3x) but of course when you can parallelize it, it's definitely a worthwhile tradeoff especially when it's more likely that one has a lot of lower memory clusters then one single cluster with a lot of memory and is likely to be hogged by a 479 CPU hour job. I wonder if this might encourage investigators to relook at existing data by de novo assembly. Of course it would be great if the NGS data is made public, then I guess other groups can actually do the de novo assembly comparison for them.

What's the difference between an accession number (AC) and the entry name (ID)?

2012-01-20T01:06:00.000+08:00

RT @pride_ebi: .@uniprot 101: What's the difference between an accession number (AC) and the entry name (ID)? http://www.uniprot.org/faq/6

Read it online: http://twitter.com/emblebi/status/154584407729119233

Cancer Commons is a non-profit open science initiative dedicated to improving outcomes for today's cancer patients.

2012-01-20T00:32:00.000+08:00

This should be interesting to watch out for ...

http://cancercommons.org/about/

cancercommons.org/

Cancer Commons is a non-profit open science initiative dedicated to improving outcomes for today's cancer patients. Our goals are to: 1) give each patient the .