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You might try out MedWorm too

frankie — Mon, 19 Nov 2007 00:17:08 -0500

A nice introduction to Yahoo Pipes. You might also try out MedWorm which allows you to create RSS feeds from queries on its sources - which currently includes over 5000 medically related RSS feeds (sorry, I too am recommending my own site - which is where I came across this posting, since I like to keep a check on blog postings tagged with 'RSS' - I hope you may excuse this since the site is highly relevant to this posting).

Scintilla

alf — Fri, 16 Nov 2007 05:43:28 -0500

For the science side of things you could give Scintilla a try (sorry for plugging my own site, but it is designed for this kind of thing: if it doesn't suit the way you work then let me know).

that works too,,,

agbiotec — Thu, 15 Nov 2007 13:58:15 -0500

,,, but on a second thought, with the Pipes you can mashup and filter RSS from any source,,, so in addition to having keyword-filtered articles from papers, you can also have blog posts, newgroups and whatever else RSS content cleansed and delivered all in a single feed,,, I guess you could also do that by searching within Google reader after you aggregate your feeds there,,,

What about PubMed?

dbtodd — Thu, 15 Nov 2007 12:32:41 -0500

If your articles of interest are there of course (and a big if here). I have a couple saved searches in PubMed and subscribe to the feeds for those searches. One of these is a long list of scientists in my field for example. I subscribe using Google Reader so new papers come through every day and scanning through them in Reader is much easier than using PubMed directly. I then use a set of labels to prioritize articles for follow up and importing into the excellent pdf manager Papers.

Pipes are pretty nifty

pwnedd — Thu, 15 Nov 2007 10:33:28 -0500

Pipes are pretty nifty indeed. I created one for the same purpose myself a little while back for filtering items from a few different journals. I've since thought of an even easier way to search through a large number of journal feeds, but have not had the time to blog about it lately because I've been so caught-up in school work. Basically though, the idea is to combine google reader + yahoo pipes. Yahoo pipes is powerful, but it is a pain to handle a high number of feeds. It is very easy to add feeds to google reader however, so rather than adding the feeds directly to yahoo pipes, you could instead create a google reader account just for journal feeds. Give them all a tag like "article," and then feed your google reader "article" feed (which will include all items from all of the journals) into Yahoo pipes. This way you will only have to deal with a single feed in Yahoo pipes, and adding new journals becomes trivial.

Not bad, huh? :)
Keith

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

Good ideas, now we need details

Neil — Thu, 15 Feb 2007 22:54:11 -0500

I think the idea of a wiki for collaborative annotation appeals to a lot of people. The discussion around your post highlights the challenge: we have to go beyond the idea to the details of the implementation, i.e. the software engineering.

It would be hopelessly inefficient to rely entirely on manual annotation and the efforts of users. A wiki would somehow need to capture data from existing sources (sequence databases + automated annotation) and present it to the user for editing. There would have to be rules (ontologies) and a way to agree on a final annotation (voting? approval by an expert?)

I guess we're looking for a combination of the functionality of the IMG, the ideas of manatee (but not the implementation) and the philosophy of wiki.

Thank you Neil, and well

Greg — Mon, 29 May 2006 07:48:13 -0400

Thank you Neil, and well said by the way. I'm not sure if it is the promise of lucrative jobs or lack of jobs (IT jobs are becoming a commodity ?) in IT that is driving people to search for information on computational biology. My current take on the lucrative jobs aspect is that from the outside looking in computational biology superficially has all the attributes of the next big ICT boom: large amounts of data, the need for people with IT/CS skills, novel method development, application of statistics, potential to lead to new drug development and medical breakthroughs etc. This leads people to believe that it will be the a ticket to fame fortune and glory.

Of we on the inside know that one point of failure in this little fantasy is lack of standards for biological data. My argument is that the incentives are just not there for biologists to work together on formal standards for the life sciences (it is all about discovery). Industry is also not that focused because the market is just not big enough. While microarrays are good business, mobile phones eclipse them by many orders of magnitudes. I don't doubt that the situation will get better, just not as quickly as you would imagine. What it boils down to is that lack of standards makes it hard to commoditize the knowledge necessary to working computational biology. Hence producing humans with standard compbio knowledge to fit into standard jobs is not possible.

But it goes both ways.

People on the inside looking out haven't yet appreciated the need to *pay* good money for people with IT/CS skills to make their computational pipelines more robust/extensible. It is publish or perish all the way, not re-factor and thrive.

IT market

Neil — Sat, 20 May 2006 06:39:53 -0400

My naive assumption would be that you're seeing IT graduates in search of employment. India and SE Asia have seen a huge increase in IT investment and education in recent years and many graduates are under the impression that biology is a source of lucrative jobs. Recall when the human genome project neared completion - there was much hype about disease gene discovery, cross-fertilisation of the IT and pharmaceutical sectors, even dire predictions that the amount of data would be too great for current hardware.

As it turns out, identifying genes is just the first tiny step in any kind of biomedical advance and whilst we can certainly handle the raw data, extracting what we want from it is immensely painful due to inadequate data standards and integration. And now I hand over to Greg :)

If you look at google

maximilianh — Sat, 20 May 2006 05:47:51 -0400

If you look at google trends, almost all queries for "bioinformatics" come from India! The list is INDIA (5 times more than number two), Singapore, Korea, Malaysia, then, heck, Ireland! United States are ranked 8th on this list!
"Football" immeditely gives United Kingdom, Biology quickly UK/US, but "molecular biology" again gives India, Korea etc. Any ideas? Is India so much stronger in "molecular biology" and "bioinformatics" than these other countries or why do people type in these keywords into google, if not?

GTrends

PedroBeltrao — Fri, 12 May 2006 05:01:54 -0400

The time we can waste on Google trends :). I gave it a go as well but it is a pity that they don't have an option to restrict to the search volume of Google Scholar. Maybe there are not enough searches there to make these trends. This way the trends don't really represent the scientific view of these terms. We don't really see in GTrends the buzzword chasing phenomena when you try to compare the different keywords (like genomics, proteomics, systems biology, synthetic biology).
Go give Co-Op a try, it is a bit obscure but there might be something there of use. You can tag online content and make your meta-data available for subscription to anyone (social search). I am not sure that you can access the meta-data trough the normal Google web API but if it is possible than there might be some interesting uses for it. If we can't use the API then it will be again like Google Base (only potentially useful)

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...