nodalpoint.org

If you are interested in running a Drupal site with PubMed content you should check the screencast below. It explains how it can be done with existing Drupal modules. I'm working with a student from the University of Szeged on a PubMed module for Drupal. So in the future this should become a bit more straightforward ;)

Hi,
python 2.6 is going to implement a new kind of data (like lists, strings, etc..) called 'named_tuple'.
It is intended to be a better data format to be used when parsing record files and databases.

You can download the recipe from here (it should be included experimentally in python 2.6):
- http://code.activestate.com/recipes/500261/

Basically, you instantiate a named_tuple object with this syntax:

> Person = NamedTuple("Person name surname")

"Person" is a label for the named_tuple; the following fields, 'name' and 'surname'

Scientists usually share information with collaborators from all around the world. For that purpose, eyeOS (www.eyeos.org) provides an invaluable system to access and share documents, create and save data files or store crucial personal and professional information.

To see eyeOS widely used by scientists all around the world, we initiated the eyeLIMS project ! eyeLIMS is a community-driven project which aims at providing a Free, web-based, Open Source Laboratory Information Management System (LIMS) powered by eyeOS.

After a long hiatus SciView is back with a new interview with Dr Roderic Page from the University of Glasgow. Dr Page is the current Editor in Chief of Syatematic Biology and developer of TreeView(X), the beloved phylogenetic tree visualization software. He was also the editor of the Current Protocols in Bioinformatics.

As usual here is the link.

Enjoy.

I decided to jump on the bandwagon, the same Rosie Redfield jumped because of Pedro: Open Science.

Reading the article Gene Wiki conceptual overview posted at TSL on Nodalpoint some time ago, and looking in the proposal made there, I wonder if this is not already being done. There is the BOWiki Project. BOWiki extends a Semantic MediaWiki by additional functionality to allow the annotation of gene data and is supposed to allow the curation of biomedical ontologies as well. It makes heavy use of biomedical ontologies in the description of genes and gene functions, in order to allow a search of the wiki using the categories in the ontologies.

We just posted an overview document of our idea for a Gene Wiki at The Synaptic Leap

We encourage all folks at Nodal Point to come and add their comments. To maximize our feedback (the more the better), I have removed the login restrictions for comments for a brief period.

Thanks in advance for helping us out.
-Ginger

I recently downloaded Medline in XML format - the goal is to load it in a relational database (like mySQL), index it, and then somehow save the world with the data. I'm pretty sure tons (relatively speaking) of people have done the same thing before (except maybe the save the world part), and I'd prefer not to reinvent the wheel if I don't have to.

Anyone know of a good XML->database parser for Medline? If not I guess I'll code one myself! Indexing tips / advice would also be appreciated (first time I'm playing with a 50+ GB database). I heard Lucene is the bomb for indexing such a large database...

I'm the founder of The Synaptic Leap We're also using Drupal. Our site has been live since late November. I'm coming out to the SF Bay Area May 30 - June 6. Is anybody maintaining NodalPoint interested in getting together to discuss possible synergies and philosophies?

Email me or reply to the post to discuss.

(Via chem-bla-ics and Yakafon)

BioMed Central will be hosting a new journal entitled "Source Code for Biology and Medicine". According to journal description:
Source Code for Biology and Medicine aims to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.