how to start a Galaxy session on the web pages:
by Vestrheim Olav
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
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15 years, 3 months
Announcement: Wikiomics - http://wikiomics.org] (fwd)
by Belinda M. Giardine
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 -------
15 years, 3 months
ideas from using Galaxy2
by Belinda M. Giardine
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
15 years, 3 months
Fwd: Re: other "random" problems
by Cathy Riemer
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 -----
15 years, 3 months
test
by Anton Nekrutenko
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
15 years, 3 months
other "random" problems
by Belinda M. Giardine
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
15 years, 3 months
Fwd: [Fwd: mail failed, returning to sender]
by Anton Nekrutenko
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
>
15 years, 3 months
