I think in general you should make sure to cite the authors of the original publication in addition to Galaxy, the note in Galaxy should make this explicit.

Absolutely agree, the citations are arguably the most important part. The GeneTrack paper citation is currently listed in the help for the tools at http://usegalaxy.org and in -central. Any place where a citation is missing is an error and will be corrected as soon as it is reported. Thanks for using Galaxy, Dan On Nov 10, 2011, at 12:55 PM, Istvan Albert wrote:

Hello Everyone,

...

Galaxy tells me to "cite Blankenberg D, et al. In preparation."

I think in general you should make sure to cite the authors of the original publication in addition to Galaxy, the note in Galaxy should make this explicit.

Small tidbits that may be useful. There is a command line version for genetrack with its source code at:

https://github.com/ialbert/chipexo

this is a fork of my son's project while he rotated in a lab, he ported a number of tools including GeneTrack to a command line interface. Seems to work well but I have not ran it for large genomes.

In the course that I teach the lectures covering ChipSeq analysis: 19, 20 and 21 cover the usage and principles of GeneTrack (among other topics)

http://bcc.bx.psu.edu/courses/597D-2011/index-597D-2011.html

best regards,

Istvan

On Thu, Nov 10, 2011 at 12:19 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:

...

Hi Steffi, GeneTrack should be working again on the Main server, thanks for reporting the error. For information on the inner workings of GeneTrack, you should consult the paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you can additionally contact the GeneTrack author, who I've CC'd here.

Thanks for using Galaxy, Dan

On Nov 10, 2011, at 11:32 AM, Stefanie Ververs wrote:

Hi everybody,

I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. I still have some questions:

1) Am I correct that the genetrack indexer seems to be down on the Public Galaxy Server? I get a server error, when I start it. (The Genetrack Browser doesn't work either; although I'm still not quite sure whether there are dependencies.)

2) By now, I know one paper on Genetrack - http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I found the following presentation slides: http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy tells me to "cite Blankenberg D, et al. In preparation."

Is there additional information? It would be great to know how exactly the peak predictor works, but the slides give only a kind of overview, but of course no explaining and no details and the paper isn't that clear.

Thanks,

Steffi ___________________________________________________________ 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:

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-- Istvan Albert Associate Professor, Bioinformatics Pennsylvania State University http://www.personal.psu.edu/iua1/