marcius's blog

16 Feb

postgenomics.com

Published by marcius

This is really interesting. We certainly should try to get some of that working within TDI/TSL!

16 Feb

Wikis for genomic research

Published by marcius

Community 

general open research

Few days ago, Nature received that article which sparkle some intense debate in the BioMed community: Gene-function wiki would let biologists pool worldwide resources : Nature: "As a frequent user of Wikipedia and also a biologist, I hope that one day a wiki on gene function will be voluntarily created and maintained by biologists." At TDI/TSL We have envisioned what we call the "GeneCards" that will collect all available information (mostly from NCBI) about a given gene. Then users of the community would be able to do several things with the cards: i) VISUALIZE. Users will be able to see what a gene card has to say about a given gene. Imagine being able to visualize centralized data for a given gene. ii) MODIFY. Users will be able to add information. Imagine a GeneWiki specialized for biological data entry. iii) LINK. Users will be able to (using bookmarklets) link pieces of information in the web to a given gene (including pubmed entries). Imagine Connotea/CiteUlike with a third dimension (user/data/gene). iv) "OWN". Users will be able to save a GeneCard into their "baskets" and associated data to them (such as tags). Imagine Flickr for genes. Of course, all of this is just in our imagination for now (and still for some time). We are planning to develop de needed modules within Drupal and initially apply them to the malaria genome. Any help is welcome! ;-) Best! marc

15 Feb

Gene Wiki Programmers Needed

Published by marcius

Subject 

Request for Help

TDI and TSL are in need of volunteers for the tools development within the Malaria community. You can read about the projects themselves here. So, what we need? Basically, we seek programmers with an interest of being part of a new community for BioMedical research. You would be applying your skills to develop tools that that should help advance the research of drug discovery for neglected diseases. This is something that you will feel good about! Gives good Karma!! The skills we are looking for in a volunteer in those projects are: - JavaScripting (in particular bookmarklets) - PHP programmer - MySql database experience - Familiarity developing Wiki-based tools a strong plus. - Familiarity with Drupal a strong plus - Familiarity with Trac a strong plus - Familiarity with Subversion a strong plus If you see that you would like to join, please do so by posting a comment to this entry! Thanks! marc

15 Feb

Some reading...

Published by marcius

Subject 

Miscellaneous

This is some reading you guys can do for getting familiarize on what we intend to do with TDI and TSL. I have posted in our respective web sites a one-page flyer with the very basic information:

TSL flyer
TDI flyer

You can also read the manuscript that started it all... Maurer, Arti Rai and Andrej Sali, PLoS Medicine 2004 and the commentary in The Economist about this manuscript.

Best,
Marc

14 Feb

European Parliament Hearing on Neglected Diseases

Published by marcius

Subject 

External News

European Parliament Hearing on Neglected Diseases - European Public Health Alliance:
The hearing seeks to highlight the need for better regulatory practices which are more suitably adapted to assessing therapeutic advances of new drugs, vaccines and diagnostics for neglected diseases. These diseases include AIDS, malaria, tuberculosis, leishmansis, Chagas disease and sleeping sickness.

14 Feb

TDI/TSL presented in Stanford University

Published by marcius

I have been introducing to the Stanford medical students what we do for the TDI and TSL initiatives. Achal S. Achrol is organizing a series of talks on Neglected Diseases and invited me to talk about our initiatives. You can see the slides here. I think that the audience was quite interested in the approach we are taking and hope we will have some of the folks joining TSL/TDI in a near future.

Achal and his collegues are very interested in implementing a wet-lab open-research community where scientists are able to share resources and information for a common goal... accelerating the drug discovery process for neglected diseases. There is certainly a good possibility of collaborating with them within the TSL initiative.

marc