nodalpoint.org - Markup languages - Comments

Content

alf — Thu, 19 Apr 2007 05:34:45 -0400

If you can define more precisely the types of content you'll want to log, that would make it easier to point to useful plugins/modules.

use a blog to follow a project of bioinformatics

dalloliogm — Wed, 18 Apr 2007 09:18:02 -0400

I would like to do the same thing as you with notepress: use a blog to follow a project of bioinformatics.

I'm a last-year degree student and I have to follow a short period of practice of six-months in a research laboratory; the project I will work on is an analysis of the secundary structure of some genes in yeast.
Since I'm fond of Internet and the web 2.0 stuff, my head laboratory agreed to let me work slower on my project, allowing me to spend more time on deciding how to organize it and how to present it.
I've also had had to present a seminar a few weeks ago, you can find it here: http://genome.imim.es/~giovanni/ .

so I'm trying with a wordpress blog running on my local computer: I'm using it to collect all the resources on Internet, the workflows I'm using and to take note of the progresses I make.
Actually I'm not very good with the technical part, as I'm not sure I've understood very well what COinS is and I've not tried Drupal yet (I will study ;) ).

So I was looking for some interesting plugins for wordpress: in particular, I would like to find something to manage reviews on articles and resources on Internet, and maybe to implement a connotea/citeulike/other(zotero when it will have social bookmarking utilities?) account, but I believe I won't find very much :(

What kind of thing are you

alf — Tue, 17 Apr 2007 05:13:20 -0400

What kind of thing are you trying to do? There's a COinS plugin for Wordpress that does a little bit of this, but it's not proper structured blogging. You might be better off using Drupal and defining your own CCK content types.

Structure Blogging Plugin

dalloliogm — Mon, 16 Apr 2007 10:43:15 -0400

Hi,
I was trying out this plugin, but it seems that it doesn't work anymore, it is not compatible with wordpress 2.1 and the developers aren't going to continue it (http://mail.structuredblogging.org/mailman/private/structuredblogging-di...).

Moreover, the page referred for the other plugin Notepress, is not avaible any more http://projects.hubmed.org/track/notepress :(

---

http://genome.imim.es/~giovanni

REST and recuperation

Duncan — Tue, 06 Jun 2006 06:00:59 -0400

Thanks Greg, I'm glad someone is enjoying my rambling posts to nodalpoint!

I don't know why there aren't more REST style services out there, why has everyone plumped for the "over-engineering" of SOAP+WSDL? Maybe its because many of these services are provided by large government-funded bodies like the NCBI and EBI who employ professional software engineers (not bioinformatics hackers) to deploy these services. Many software engineers like big complicatd over-engineered solutions that only they truly understand :)

I think the NCBI method of supplying both REST as well as SOAP+WSDL is a sensible one, you choose the interface that you like best, rather than the "one true interface"...

Firstly, thank you for all

Greg — Sun, 04 Jun 2006 23:10:44 -0400

Firstly, thank you for all these great posts, you're putting us regulars all to shame.

many publicly available biomedical services, are not the simpler RESTian type, but the more complex SOAP-and-WSDL type of web service.

For as long as I have been doing this I've always felt that most in-the-trenches bioinformatics hackers would be vehemently opposed to the over engineering that is SOAP+WSDL and prefer the intuitive and straight forward REST style. NCBI's EUtils looks like the only game in town if you want REST based webservices, everything else as you point out is based on SOAP. Why is that ?

IIRC Henry S. Thompson was

Greg — Mon, 29 May 2006 10:06:56 -0400

IIRC Henry S. Thompson was behind XML Schema, which hasn't exactly been a resounding success. Also the misuse of the term microformat was also annoying (RSS is not a microformat). Nonetheless it was an amusing read, thanks for pointing it out.

Harry Haplin also has a blog.

glad you enjoyed it

Duncan — Thu, 25 May 2006 05:10:42 -0400

Hi Neil, glad you enjoyed it. The other papers at www2006 are a good read too, the quality of this conference seems to be getting better every year...

Good read

Neil — Wed, 24 May 2006 21:49:45 -0400

I enjoyed the paper (nice post too by the way); it's informative, interesting and very readable. Everything that most technical literature on XML/semantic web normally is not :)

I just tested out the new

Greg — Wed, 25 Jan 2006 05:43:52 -0500

I just tested out the new plugins with the PubMed lookup functionality. Very very nice. A similar structured blogging plugin for Drupal would be nice.

I notice that the Wordpress plugins seem to recreate their own editing interfaces (the WYSIWYG editor is not enabled for the Review template).

Theoretically this should be easier in Drupal...

Neat

chris — Fri, 13 Jan 2006 15:41:52 -0500

Thanks alf, that's very cute. Definitely makes life easier.

Here are some files that

alf — Thu, 12 Jan 2006 16:13:01 -0500

Chris, here are some files that will let you look up PubMed articles by title and automatically fill in the metadata.

Lab notebook blogging

Neil — Wed, 11 Jan 2006 21:10:53 -0500

I've been wondering how difficult it would be to prescribe a standard format for entering the methods and results of scientific experiments into a weblog...

Me too. One day I hope to get back to working on MamboLIMS and add some more features. One would be the addition of Mamblog, which is a rather simple blog component for Mambo but would be suitable as a basic research diary. A second idea would be to develop an electronic lab notebook using Facile Forms as for the other LIMS forms.

Standardisation could work well for certain types of experiment - assuming that most people are doing experiments in molecular biology (cloning, expression) or biochemistry (assays, purifications). You'd need form fields along the following lines:

Date and time
User name (and some permissions system to link user to experiment)
Aims of experiment
Protocol or a link to an SOP
"Results" being the tricky part (see below)
Text field for conclusions, musings about further work

Results is obviously the hard part to standardise, as results can take many forms. It may be easiest to think of results as separate files, then the form can ask "how many do you have" and provide facility to upload any kind of file format - images (for gel photos), spreadsheets or delimited text (for assays or other numerical data) and so on.

All for another day for me. Incidentally, development using Mambo has become somewhat complicated as the project has forked to create Joomla. At this stage the code seems near-identical; I'm sticking with Mambo for now.

I'm in the process of making

alf — Wed, 11 Jan 2006 19:28:55 -0500

I'm in the process of making a Notepress bundle with Wordpress 2.0 and the Structured Blogging plugin included, hopefully this week.

As for automatically filling in the form details I agree, that would be nice too.

Sounds good

chris — Wed, 11 Jan 2006 11:56:33 -0500

I've been meaning to migrate to WP for a while, and this pretty much clinches it for me. I tried writing article reviews freehand in MT, which was painful and slow.

Notepress is a definite, too.

Update
Installing both notepress and the structured blogging plugin was pretty painless. Now if the SB plug-in could automagically take HubMed urls and markup the article so I don't have to manually enter the details...