general open research

general content regarding open source biomedical research

17 Mar

TDI & TSL mentioned in The Economist article on Open Source

Published by gtaylor

Community 

general open research

Subject 

External News

Open, but not as usual mentions both Tropical Disease Initiative and The Synaptic Leap.

...Other projects, such as the Tropical Disease Initiative and the Synaptic Leap, are forming along similar lines. Synaptic Leap points out that because it is not motivated by profit, it has no motive to keep secret any fruits derived from collaboration in research on, for example, malaria....

It's nice to see us in the news of such a credible magazine. I've long been a fan of The Economist as the best way to get news with a minimum US bias. Both Stephen Maurer and Arti Rai, our advisors and founding members of Tropical Disease Initiatve, have contacts at The Economist. I assume that is how they have heard of us. 

Anyway, nice to see our name in print. I must admit I did a little dance. 

13 Mar

Ways to get involved and the Stanford Connection

Published by MatTodd

Community 

general open research

Subject 

Request for Help

A few of us have recently been talking via email about exciting developments at Stanford, and Ginger prompted me to post this on the site so others could comment. Here are the emails, edited down…

Marc originally visited Stanford to talk on what he's doing in the area of neglected diseases (http://www.salilab.org/~marcius/home/?page=talks). His talk was hosted by Achal Acrol.

In response, Achal wrote:

 

“I think it was clear that today's audience was very excited by your talk, and in general through my work with ADEM [Access and Delivery of Essential Medicines] I have noticed a growing interest here at Stanford among young researchers to carry out their training and career development in traditional ways while somehow finding some other way to simultaneously apply those skills/resources to affect some amount of positive change in the world.

 

I see probably the most effective collaboration of our efforts to be that while I continue to sign up labs that would be willing to provide certain resources and services, you could provide us with a wish-list of biological/chemical resources you would need to fully test any of the computational work your team does. In essence I would work to provide (the other 95%) 'beta-testers' that could respond to your computational biologists 'programming core' and perform the wet lab experiments and cell culture and in vivo experiments to verify in an open source manner the efficacy of those agents.

10 Mar

TSL Status March 14, 2006

Published by gtaylor

Community 

general open research

Presentation given at Stanford

Marc A. Marti Renom is by far our biggest evangelist and his efforts are making a big impact. He recently gave a presentation at Stanford talking about the goals and objectives of The Synaptic Leap and Tropical Disease Initiative. Marc posted a brief description as well as the presentation he gave this tsl post. The great news is that people at Stanford are emailing other people participating on The Synaptic Leap and they looking to find the appropriate way to get involved. Mat posted a bit of that exchange here: Ways to get involved and the Stanford connection.

Marketing observation and future objective

An interesting observation from this is that shortly after Marc gave the presentation, I noticed a spike in user activity - both more people browsing as well as a few new registered users from Stanford as well as people from Germany and Italy. We saw a similar spike in activity after Marc spoke at a QB3 Neglected Diseases symposium. In fact it was after the symposium that we were blogged about on World Changing. That in turn led to a spike in user activity.

23 Feb

New Feature for Resources Needed

Published by gtaylor

Community 

general open research

About two weeks ago Marc and I were about how we needed to make the site more actionable to get people knowing what they can do to help. I therefore have added a new menu item on the left called resources needed. When you go to that page, you will see a list of postings for resources. At the top of the page is a "sticky" page that describes for readers what they are seeing, how they can volunteer and how they can ask for help on their project. Think of this as the classified for open source biomedical research.

TSL Programmers Needed

Published by gtaylor on 23 February 2006 - 3:51pm

Community 

general open research

Subject 

Request for Help

I need at least one software programmer with the following skills:

  • PHP programmer
  • Unix shell scripts
  • MySql administration experience
  • System administration experience with development and production environments, backup/restore...
  • Familiarity with Drupal a strong plus
  • Familiarity with Trac a strong plus
  • Familiarity with Subversion a strong plus

If you're interested in potentially helping out, login and post a comment below. If you have further questions, email gtaylor@thesynapticleap.org.

 

Project overview

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

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

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