The free MS Sashimi tools at sourceforge which convert multiple vendor formats
into mzXML do *not* always work as promised (however are the best I have seen)
Sashimi is one of the most active science projects on SF. If you have
found any bugs, please submit them to the developers. As it says on
Dear all
The Blue Obelisk wiki/website has moved to http://blueobelisk.sf.net.
There were some difficulties so all user accounts will have to be
recreated. You should use the same user name for your account as
originally used, if possible.
Please let me know if there are any problems. For the re
On 01/06/07, Tobias Kind <[EMAIL PROTECTED]> wrote:
Hi Noel,
Thanks for the links. Regarding the BO WIKI I think it should be possible
to edit content for registered and known and active people. Web 2.0 time!
So if I want to add some stuff on the news page
It should posibble for me to do that a
Tobias,
Thanks for the feedback. We will take your comments on board, and
provide a number of means to read and contribute to the BO mailing
list. And even more importantly, we will advertise these means on the
various web sites, which we don't currently do.
Apart from subscribing to the mailing
Hello,
I'd appreciate if someone could beta test and give me some feedback on
a new Greasemonkey script at
http://userscripts.org/scripts/show/9526
All you need is a Connotea account. Once the script is installed, you
just navigate to a journal page, enter your Connotea username and
password, an
I would appreciate being added as a developer to the BO project on SF.
I will use this to version any Greasemonkey scripts I'm working on.
I'll make a top-level Greasemonkey folder if this is okay with
everyone (I'll put trunk, branches, tags inside this).
Regards,
Noel
___
crit:
> On May 7, 2007, at 5:39 PM, Noel O'Boyle wrote:
> > Do others agree? Several universities (e.g. Cambridge) provide Mailman
> > mailing lists so it shouldn't be difficult to find a suitable location
> > with zero maintenance required.
>
> I'
Considering the upcoming closure of CUBIC (as I understand it) could I
suggest moving the BO mailing list? For a number of months it has been
impossible to subscribe to the mailing via the web interface, which
means that we may have lost a number of potential contributors.
Do others agree? Severa
OK, thanks - it's working now...I'm behind a proxy:
server = WSDL.Proxy(wsdlFile, http_proxy="myproxy.cam.ac.uk:3129")
On 27/04/07, Rajarshi Guha <[EMAIL PROTECTED]> wrote:
On Fri, 2007-04-27 at 13:49 +0100, Noel O'Boyle wrote:
> Before trying it in Ja
ture?wsdl'
server = WSDL.Proxy(wsdlFile)
print server.getSimilesByCID(['801'])
Regards,
Noel
On 23/04/07, Rajarshi Guha <[EMAIL PROTECTED]> wrote:
On Mon, 2007-04-23 at 10:08 +0100, Noel O'Boyle wrote:
> The good thing about this is that it's easy to do and ligh
I don't see any mention of the Blue Obelisk Awards...
On 27/04/07, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
I've spent an hour on it and done about as much as I can...here are
some comments:
(1) The miscellanous links should be tidied up; there are several
pages with dupl
I've spent an hour on it and done about as much as I can...here are
some comments:
(1) The miscellanous links should be tidied up; there are several
pages with duplicate information
(2) Wiki page titles should include spaces; I've changed a few
(3) I hope I don't offend anyone by removing the a
The Blue Obelisk wiki is the public face of the BO to the world. There
has been some talk recently about promoting the BO, and this is the
website that people come to if they are curious or want to get
involved. Since it has grown organically as wikis tend to do, it is
now in need of a major revam
However I'm hitting a wall when it comes to web services that return
anything but a String when using the Mozilla SOAP api.
Does anybody have any experience with the Mozilla SOAP api?
I'm afraid not...just with JSON. The Chemical Blogspace with Quotes
user script communicates with CB using JS
Hello all,
To quote from my new blog:
"I've decided to join the ranks of blue obelisk bloggers (bloblogs?)
after realising that it gives me an excuse not to update my webage.
I'll be talking about open chemistry software, and various random
codings I'm involved in."
Could I be added to Planet BO
I've written a new version of the greasemonkey script for connecting
the DOIs on table of contents pages and chemical blogspace. This one
has a bit more 'wow' to it. :-) It is best explained by the screenshot
at the bottom of:
"http://wiki.cubic.uni-koeln.de/bowiki/index.php/Using_Javascript_and_
Could someone please disable anonymous edits on the BO wiki, and
revert recent spam?
Noel
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Nature Methods editorial recommends availability of source code...
http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html
Noel
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Are people aware of MCDL?
http://www.mdpi.org/molecules/papers/11040219-old.pdf
This might help with 2D structure diagram generation
Noel
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I've moved all of my instructions regarding Javascript and
Greasemonkey to the BO wiki here:
http://wiki.cubic.uni-koeln.de/bowiki/index.php/Using_Javascript_and_Greasemonkey_for_Chemistry
Unfortunately, the JACS TOC jpg does not appear. Can anyone figure out why?
Noel
_
BTW, Noel, it might be interesting to look at that script I linked to in the
other reply, which actually puts content from PG in the TOC of the journal.
Since Cb is based on the PG software, the API should be the same.
Egon
1.http://chem-bla-ics.blogspot.com/2006/12/smiles-cas-and-inchi-in-blogs
On 17/03/07, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
What would you like to see on a Blue Obelisk Firefox toolbar? Here are
some ideas, some of which I think are trivial to implement, would be
instantly useful and greatly increase our world domination:
(1) Click on the little pro
On 17/03/07, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
What would you like to see on a Blue Obelisk Firefox toolbar? Here are
some ideas, some of which I think are trivial to implement, would be
instantly useful and greatly increase our world domination:
(1) Click on the little pro
What would you like to see on a Blue Obelisk Firefox toolbar? Here are
some ideas, some of which I think are trivial to implement, would be
instantly useful and greatly increase our world domination:
(1) Click on the little protein button, and all pdb codes in the text
become highlighted, and cha
Considering the recent release of the Chemical Test File Repository, I
was wondering whether BODR is interested in comp chem log files. I
create a release every so often of the comp chem log files that have
historically broken cclib. In this way, these log files define the
parsers used in cclib, a
From Nature 8-Feb-07:
Campaigning for open access gets easier
Organizers of an Internet petition supporting free access to scientific
results have hit a nerve. Nearly 18,000 people and institutions have
signed up since 17 January. "I think it is one of those interesting
viral network sort of eff
Maybe some of you can think up of some nice uses for Yahoo Pipes,
which seems to be a "Pipeline Pilot for RSS feeds":
http://pipes.yahoo.com
Regards,
Noel
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gElemental (a fork of gPeriodic) got a write up in the latest Linux
Format (available on paper only). One of the coming attractions is
integration of the BODR, which is mentioned in the review as a very
positive idea...
Noel
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Not to disagree with your main points, but in relation to European
bodies promoting open data, the European Bioinformatics Institute has
the following mission statement on their web page:
"""
Our mission
* To provide freely available data and bioinformatics services to
all facets of the scient
I'm forwarding this message from a PLOS announcement list, as I think
several of you will be interested in supporting this...
Forwarded Message
From: Mark Patterson <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: PROOF: Join PLoS and Sign the EC Petition
Date: Fri, 26 Jan 200
Apologies for cross posting, but those of you who use Subversion with
sourceforge projects will probably be interested in the following
notice:
http://sourceforge.net/docs/E09/en/#notice
"""
On November 31, 2006 the access method for Subversion changed. This
document reflects those changes. The
As an aside, I note that BioJava and BioPython are completely
different. As are BioPython and BioPerl, for instance. They are not
parallel implementations of the same functionality, but different
implementations of some of the same functionality. I think we should
try to avoid this situation.
Noe
Well, I *have* to add something to this discussion, even if it's just
to reiterate the points made by Rajarshi and Geoff. :-)
I think that using the currently available cheminformatics toolkits
from Python is a much better idea than reimplementing algorithms in a
different language. For Java libr
It seems that Gmane have added blue-obelisk. You can subscribe to rss
feeds for the BO mailing list here:
http://dir.gmane.org/gmane.science.chemistry.blue-obelisk
Noel
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