nodalpoint.org - OSS - Comments

Sure

nuin — Wed, 15 Aug 2007 07:48:40 -0400

The more the better.

I am in the process of finishing a manuscript and we will start coding as soon as I finish it. I send you an email with the idea.

BTW, pretty nice application you have.

Paulo

Need some help guys?

bosco — Wed, 15 Aug 2007 03:03:43 -0400

I'd love to help out even though I'm just a structural biologist and not a sequence jockey.

I have experience programming in C++/wxWidgets: I've written a complete GUI application in that platform http://boscoh.com/ramaplot. My main platform @work is Python so I'm keen to seen how wxPython stacks up against wxWidgets.

I can help you work on the GUI aspect.

great tip

Neil — Mon, 24 Jul 2006 08:00:19 -0400

That's a great tip. Are there any neat web tricks that alf doesn't know ;)

mozex

alf — Mon, 24 Jul 2006 05:25:24 -0400

Mozex (Firefox extension) is worth a mention here too.

Marking nar tests

Neil — Sat, 22 Jul 2006 21:42:38 -0400

I thought about that (a column with a tick or something). I think it's easier if people just look for the "none yet" in the comments column. Also, there's no reason not to have >1 comment per service. Wiki editing is a freeform process - I think this troubles people who prefer a clean forms interface to a database, but I'd encourage people to give it a try. You need to get into the "wiki mindset" :)

wiki format is tricky

Neil — Sat, 22 Jul 2006 21:01:46 -0400

I just knew that someone would have this criticism :). You're quite right though - the people in my group have the same complaint about the lab wiki. I know that Twiki has a table editor plugin which provides a form interface for table editing - does dokuwiki have similar?

I did consider a forms/database solution, but wasn't sure if it was worth the time. If people are keen to contribute to this, leave comments and I'll cook something up. The good think about the wiki though, is that it's already setup for Nodal users.

In the meantime, you can always copy the wiki-formatted text to an editor and search for what you want, then paste back, I guess.

[s, |s and URLs

Stewb — Sat, 22 Jul 2006 18:42:29 -0400

You probably don't want to hear this after all that copy n' paste but the format on the wiki is a bit tricky: it's hard to find the program that you want to add a note to. :)

The wiki is a good starting

Greg — Sat, 22 Jul 2006 14:43:43 -0400

The wiki is a good starting point, but some kind of database listing these services would be better. Amazingly these resources now have a term: Resourseome. This comes from a recent perspective in PLOS compbio, Time to Organize the Bioinformatics Resourceome.

The article mentions the Bioinformatics Links Directory, which in fact has all the NAR web server issue links with categories. Of course there is no machine readable representation of the data to help avoid the copy-and-paste problem. Sigh.

Some more detail on the reasoning behind using a 'links directory' is available here. There is only one other effort I know of that catalogues biological resources: BiowareDB. I have previously toyed with using this kind of thing as a starting point for RDF descriptions of biological resources. Read more about that here.

As an aside, I find the use of "web server" annoying, it should be "web services". Maybe I'm just pedantic.

suggestion for NAR test

PedroBeltrao — Sat, 22 Jul 2006 11:13:03 -0400

Maybe we could mark the ones that we are testing so that we don't re-test stuff.

For non-fans of soccer...

Neil — Mon, 12 Jun 2006 21:08:10 -0400

I enjoyed the famous curves. If soccer* is really not your thing, I recommend this YouTube video (via BoingBoing).

* since moving to Australia, I've slipped into the habit of calling football "soccer", as "football" here means "any game where you kick a ball unless it's spherical".

As Alan suggests in the

Greg — Thu, 23 Mar 2006 00:02:53 -0500

As Alan suggests in the previous comment, the best place to ask these kinds of questions is via the SIP mailing list (I assume that is the right one ?).

zope 3.2 ?

lon1 — Wed, 22 Mar 2006 12:34:12 -0500

Is SIP running under zope3.2 ?

I am just trying to see if I can set it up running , but I got ton's of messages, and the zope instance stopped. The meaningful messages was:

ZopeXMLConfigurationError: File "/var/lib/zope3/instance/1/lib/python/sip/services/appcontainerservice.zcml", line 3.2
ConfigurationError: ('Unknown directive', u'http://namespaces.zope.org/zope', u'serviceType')

It looks like the

Thanks.

Congrats :)

PedroBeltrao — Thu, 01 Dec 2005 15:05:03 -0500

Congratulation on Greg and Nodalpoint for the good press coverage.
I personally like this sentence taken from the editorial : "few organizations seem to be aware that by making their data available under a Creative Commons licence (see http://creativecommons.org/license), they can stipulate both rights and credits for the reuse of data..."
umm ... does this mean they will move to a creative common licence soon ?

Sample Inventory Program (SIP) Answers

alanrunyan — Wed, 09 Nov 2005 10:41:33 -0500

Aaron,

Best place is to ask on the sip mailing list.

I just re-read the README documentation. Yes, if you have no clue about Zope3 and how to install software you would not have much success. There *is* some upside: There are 2 deadtree books on Zope 3!

Regarding punters i.e. online demo: you can try http://sip.houston.enfoldsystems.com with the login/password, gandalf/123

Regarding QT client, since that is being developed at SFBR and outside of Enfold Systems, I do not know. They are using it in production and it probably needs quite a bit of refactoring for general consumption.

The problem is that it takes a very long time to make software usable out-of-the-box. We are hoping to go for a grant and get the NIH to pony up money for us to create a windows installer that ships with postgresql. one click install. We are very successful with the Plone Windows installer -- as an example of ease-of-use.

Thanks for your questions,
Alan Runyan
Enfold Systems
SIP, an Open Source LIMS

SIP questions

ajeffs — Mon, 07 Nov 2005 21:32:49 -0500

Alan,

Any idea when install docs with more detail than the readme in the SIP tarball will become available? Also, any chance of Enfold setting up a demo system for punters to test without having to perform a local install? Any idea when the Qt client will be out?

Aaron.