January 2006 - galaxy-user - lists.galaxyproject.org

how to start a Galaxy session on the web pages:
by Vestrheim Olav 31 Jan '06

31 Jan '06

are you online with this pages, there are so many losse ends, so I wonder if there are any possibilities to do a galaxy search and analysis on the web, and test the porgram before I do the home innstallation. best regards Olav vestrheim ------------------------------------------------------------------------------- This verifies that this e-mail has been scanned for virus and deemed virus-free according to Bitdefender and Norman scan engines. 30/1/2006 -------------------------------------------------------------------------------

2 1

Announcement: Wikiomics - http://wikiomics.org] (fwd)
by Belinda M. Giardine 27 Jan '06

27 Jan '06

Just in case you are interested. Belinda ---------- Forwarded message ---------- Wikiomics is an open documentation initiative in the field of bioinformatics and systems biology. Wikiomics consists in a free space for storing and sharing information that joins together practical and theoretical aspects of bioinformatics. Anyone can initiate or modify an article at Wikiomics and use it as a collection of notes, links and papers on a specific problem. Page history and email notification make it easy to track changes made by other users of this wiki. Each article of Wikiomics is a dynamic, easy-to-maintain review which would eventually provide: - - brief explanations of strategies and methods, possibly with figures and math formulas - - links to relevant bioinformatics services and software distributors - - links to PubMed abstracts, thanks to a built-in citation manager So make yourself at home at http://wikiomics.org And have fun! Martin Jambon, for the Wikiomics technical staff. - -- Martin Jambon, PhD Keep up with Bioinformatics at http://wikiomics.org ------- End of forwarded message -------

1 0

ideas from using Galaxy2
by Belinda M. Giardine 24 Jan '06

24 Jan '06

While I was trying to do an example showing Galaxy2, I found myself looking for tools that weren't available. When working with the mutations it would be nice to have some function for getting exact matches, possibly even using the name field. When the data is mixed with very large and very small regions just overlap isn't always to most informative. Mutations also give you up to 3 names for a single nt region. It would take incorporating the name field to distinguish these. Also when it comes to looking at the queries there is nothing for displaying more than 1 at a time. It would be nice to be able to view them as multiple user tracks at UCSC. Also graphs that show more than 1 query? I would have liked somehow either graph or at least a number in a column to be able to get a count of the number of regions that overlapped each region in a second query. Similar to coverage but with counts. Belinda

2 2

javascript error
by Belinda M. Giardine 21 Jan '06

21 Jan '06

Using Firefox on Windows, Galaxy site linked from bx home page. In JavaScript Console Error: wipeIn is not defined Source File: http://g2.bx.psu.edu:9000/tool_menu Line: 22 Plus same error for WipeOut. Belinda

1 0

Fwd: Re: other "random" problems
by Cathy Riemer 19 Jan '06

19 Jan '06

Istvan, To respond to Belinda you need to include her address, as she isn't subscribed to the Galaxy-user list. I imagine this will be true of most users who send mail to this address. -Cathy ----- Forwarded message from Istvan Albert <iua1(a)psu.edu> ----- Date: Wed, 18 Jan 2006 09:18:17 -0500 From: Istvan Albert <iua1(a)psu.edu> To: Galaxy-user(a)bx.psu.edu Subject: Re: [Galaxy-user] other "random" problems On 17 Jan 2006 15:05:50 -0500, Belinda M. Giardine <giardine(a)bio.cse.psu.edu> wrote: > Periodically when I go back to Galaxy from the results I either get the > error text I sent the other day or no tool panel. I don't see a direct > cause or conditions when it happens. > The other thing I have been noticing that on submitting a query sometimes > the history panel doesn't refresh and I have to click refresh to get the > latest query added. Belinda, I think you computer/browser settings must be causing this. I'm not one who would be eager to jump to this conclusion just because I do not see this problem buth the magnitude of the issues, their visibility and the lack of similar reports suggests that this has to be specific to a certain browser/computer setup. Certainly the HTML/Javascript code is fairly complicated, there are some neat effects and there are plenty of workarounds that were needed to make them work identically for most browsers (not just to render properly but to also cache certain files for optimal performance). We should probably take another close look and evaulate the interface on an even broader variety of os/browser combinations. Maybe we should tone down some effects or maybe we should detect browsers and simplify the templates accordingly Istvan. -- Istvan Albert, Research Associate, Bioinformatics Consulting Center, Huck Institute for Life Sciences, Pennsylvania State University http://www.personal.psu.edu/iua1 _______________________________________________ Galaxy-user mailing list Galaxy-user(a)bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user ----- End forwarded message -----

1 0

test
by Anton Nekrutenko 19 Jan '06

19 Jan '06

TEST Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton(a)bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

1 0

other "random" problems
by Belinda M. Giardine 19 Jan '06

19 Jan '06

Periodically when I go back to Galaxy from the results I either get the error text I sent the other day or no tool panel. I don't see a direct cause or conditions when it happens. The other thing I have been noticing that on submitting a query sometimes the history panel doesn't refresh and I have to click refresh to get the latest query added. Belinda

2 1

Fwd: [Fwd: mail failed, returning to sender]
by Anton Nekrutenko 18 Jan '06

18 Jan '06

Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton(a)bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu Begin forwarded message: > From: Radek Szklarczyk <radek(a)cs.vu.nl> > Date: January 17, 2006 7:05:00 AM EST > To: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: [Fwd: mail failed, returning to sender] > > It bounces from galaxy(a)bx.psu.edu (email from the galaxy web site). > Anyway, I'd like to submit a bug report > r > > -------- Original Message -------- > Subject: mail failed, returning to sender > Date: Tue, 17 Jan 2006 12:02 +0100 > From: <MAILER-DAEMON(a)few.vu.nl> > To: radek(a)cs.vu.nl > > > > |------------------------- Failed addresses follow: > ---------------------| > <galaxy(a)bx.psu.edu> ... transport smtp: 550 <galaxy(a)bx.psu.edu>: > Recipient address rejected: User unknown in local recipient table > |------------------------- Message text follows: > ------------------------| > Received: from [130.37.31.65] (poederdoos.cs.vu.nl [130.37.31.65]) > by top.few.vu.nl with esmtp (Smail #108) > id m1Eyobm-0002XpC; Tue, 17 Jan 2006 12:02 +0100 > To: galaxy(a)bx.psu.edu > Subject: bug: genome intervals coord/documentation? > > in the help of "file upload" it says that the coords in genomic > interval file are 0-based, end exclusive. Neither of these seem to > be true, file: > > #CHROM START END STRAND > chr1 108333207 108333209 + > > Extracts the sequence > >> hg15_chr1_108333207_108333209_+ > ATG > > which is not 0-based (the same seq you can retrieve with genome > browser, which is 1-based), neither end-exclusive (3 nucleotides). > > > -- > Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek >

2 1