GATK 2.0 drops MIT licence

Sadly Broad Institute's great contribution to new generation sequencing NGS, GATK, is not open source anymore.

GATK 2.0 is moving to a mixed open/closed-source model
The complete GATK 2.0 suite will be distributed as a binary only, without source code for the newest tools. We plan to release the source code for these tools, but its unclear the timeframe for this.

Personally I dislike this movement. If reason is money there are successful business models build around open source software without the need of leaving the open source community.

Doing this sort of things is a sacrilege for many of the members of our community fighting day and night for the #OA. I can see RMS deeply depress and crying in a corner every time such a thing happens. Whatever the reason behind this change is, presumably it has been  a long meditated one. So I would expect a better explanation of why this change was needed, why keep being an open source software was impeding this goal, and what is more important, the thing that annoys me more, and  denotes poor strategic plan for such a big change "We plan to release the source code for these tools, but its unclear the timeframe for this".  Hummm, this seems to me that commitment for open source has vanished here. Even if you believe in OS, some times you are forced to make concessions to  close software but I would expect to leave clear note when and how your source code would be open again.

How come we are going to lead a war for open access journals and against patents but want to make money of our software. This seems a deadly friendly fire to me until I read a good detailed explanation of the reasons behind.

It is a good thing to have samtools around as a backup.

== follow up ==
http://pablomarin-garcia.blogspot.co.uk/2012/11/key-points-summary-in-gatk-licence.html

from July 2011 KEGG ftp access needs paid subscription even for academic users

Unfortunately the person behind Kyoto Encyclopedia of Genes and Genomes (KEEG) is reaching retirement and the main funding agency that was suporting KEGG has changed and is no longer supporting individual databases.

Therefore starting on July 1, 2011 the KEGG FTP site for academic users will be transferred from GenomeNet at Kyoto University to NPO Bioinformatics Japan, and it will be available only to paid subscribers. The publicly funded portion, the medicus directory, will continue to be freely accessible at GenomeNet.

You can read the rationale behind in this page

We will see how this affects to the Reactome guys.

NCBI pubmed 'enhanced' web site with java script is pretty but is [a bit] wrong!

At least is wrong not to have the previous interface for no-javascript browsers.

[update] the interface seems better now, but still have some issues like:

• - In the display settings, after selecting the options, the 'return key' goes to the search field not the apply button!!

• - The same for the 'send to'. Also here the interface is a slow two steps. You need to click in the option and some extra info appears at the bottom.

• - The thing that really needs to be improved is the 'collections' interface:

• After selecting some entries, and 'send to collections' you go to the following interface:

• You need to go to 'append to an existing collection' and select one. All this is a bit time consuming. I would prefer to have the collection integrated in the pubmed pages

The usability (quick access and no mouse access) is low with the new javascript interface. It has nice effects but the animations slow things and you cannot use tab/arrow to select things.


Also the myNCBI is a nice idea, but it is very slow to add entries to your libraries it is faster to use citeulike with the doi/pubmed selector bookmarklet. The send-to/collections is unusable if you want to add more than two references. You can spent the whole day waiting for pages and selecting things. It should have a list of my collections and send directly there (as when you send to the clipboard).


It could be an awesome enhancement for newbies surfers, but a bit of a hassle for power users.

The new interface is 'modern' but not yet very efficient.

I agree also with this post:
http://permalink.gmane.org/gmane.comp.lang.perl.bio.general/21519

Nice article about how to make bioinformatic questions to perlmonks

Perl Monks meditation: RFC: Bioinformatics Tutorial by BioLion

This is a nice page to guide you how to make bioinformatics questions to programmers.
http://www.perlmonks.org/?node_id=821858