Open-Source (BioMed) Research

Open source Jmol taking over the world

2006-02-26T16:30:00.000-08:00

Definitely, open-source for biological proposes is taking off. JMol is a case in point... Egon Wilighagen summarizes it in his blog

chem-bla-ics: Open source Jmol taking over the world

Technorati Tags: biology, display, open-source

postgenomic.com

2006-02-16T15:52:00.000-08:00

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

Welcome to postgenomic.com:

Postgenomic aggregates posts from life science blogs and then does useful and interesting things with that data. For example, it allows you to get an instant picture of what news stories are being heavily linked to by researchers in the medical sciences, or which papers are being cited or reviewed most often by bioinformaticians, or which buzzwords are being used the most frequently by evolutionary biologists.

It's sort of like a hot papers meeting with the entire biomed blogging community.

Technorati Tags: biology, genomics, open-source

Related sites...

2006-02-16T10:20:00.000-08:00

List of interesting sites related to the OSBMR blog (continuously updated):

Research SA [http://researchsouthafrica.blogspot.com/]

PostGenomics.com [http://www.postgenomic.com]

Nodal Point [http://nodalpoint.org/]

BioInfBlog [http://bioinfblog.blogspot.com/]

Technorati Tags: biology, blog, open-source

Gene-function wiki would let biologists pool worldwide resources : Nature

2006-02-16T00:07:00.000-08:00

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

Technorati Tags: biology, genomics, open-source

Volunteers needed...

2006-02-14T22:24:00.000-08:00

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

Technorati Tags: Neglected diseases, open-source, The synaptic leap, Tropical Disease Initiative

Some reading...

2006-02-14T20:32:00.000-08:00

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

Technorati Tags: biology, chemistry, Neglected diseases, open-source, The synaptic leap, Tropical Disease Initiative

Enantioselective Synthesis of Praziquantel | The Synaptic Leap

2006-02-14T16:56:00.000-08:00

Enantioselective Synthesis of Praziquantel | The Synaptic Leap:

Dr. Matt Todd (the leader for the Schisto community at TSL) is proposing a Enantioselective Synthesis of Praziquantel project. Please have a look!

The aim of the project is to design and execute a catalytic, asymmetric synthesis of the active enantiomer of PZQ. The synthesis must be highly efficient and low cost. It is not enough that the synthesis works because the route needs to be scaled up for multi-ton production. The object of this open source chemistry project is therefore to share synthetic strategies and results towards this target.

Technorati Tags: chemistry, Neglected diseases, open-source, The synaptic leap, Tropical Disease Initiative

European Parliament Hearing on Neglected Diseases - European Public Health Alliance

2006-02-14T01:25:00.000-08:00

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.

Technorati Tags: Neglected diseases

Let's work together | The Synaptic Leap

2006-02-14T01:12:00.000-08:00

Let's work together | The Synaptic Leap:

This is the first project by Dr. Jean-Claude Bradley within the Malaria community at TDI/TSL. If you are a chemist you should look at it ;-).

Technorati Tags: chemistry, Neglected diseases, open-source

TDI and TSL have been at Stanford

2006-02-14T00:38:00.000-08:00

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

Technorati Tags: Neglected diseases, open-source

~TDI~ the Tropical Disease Initiative.

2006-02-14T00:23:00.000-08:00

~TDI~ the Tropical Disease Initiative.:
Only about 1% of newly developed drugs are for tropical diseases, such as African sleeping sickness, dengue fever, and leishmaniasis. While patent incentives and commercial pharmaceutical houses have made Western health care the envy of the world, the commercial model only works if companies can sell enough patented products to cover their research and development (R&D) costs. The model fails in the developing world, where few patients can afford to pay patented prices for drugs.

It is easy (and correct) to say that Western governments could solve this problem by paying existing institutions to focus on cures for tropical diseases. But sadly, there is not enough political will for this to happen. In any case, grants and patent incentives were never designed with tropical diseases in mind.

Two main kinds of proposals have been suggested for tackling the problem. The first is to ask sponsors governments and charitiesto subsidize developing-country purchases at a guaranteed price. In the second approach, charities create nonprofit venture-capital firms (Virtual Pharmas), which look for promising drug candidates and then push drug development through contracts with corporate partners. In this article, we discussed the problems with these two approaches and suggest a third, open source, approach to drug development, called the Tropical Diseases Initiative (TDI). We envisage TDI as a decentralized, Web-based, community-wide effort where scientists from laboratories, universities, institutes, and corporations can work together for a common cause.

By TDI members Maurer, Arti, Sali and Marti-Renom

Technorati Tags: biology, Neglected diseases, open-source, Tropical Disease Initiative

The Synaptic Leap | Open Source Biomedical Research

2006-02-14T00:20:00.000-08:00

The Synaptic Leap | Open Source Biomedical Research:

Open Source Biomedical Research for the 21st Century
Biomedical science is indivisible. The physical and psychological barriers that divide scientific communities are ultimately artificial and counterproductive. We see online collaboration as a natural way to bridge these gaps and pool information that is currently too fragmented for anyone to use. An open, collaborative research community will find new ways to do science, answering questions that current institutions find difficult or impossible. The Synaptic Leap’s mission is to empower scientists to make the dream a reality.

Roadmap
We are beginning our journey focused on the two tropical diseases malaria and schistosomiasis. Diseases found exclusively in tropical regions predominantly afflict poor people in developing countries. The typical profit-driven pharmaceutical economic model fails with these diseases because there is simply no money to be made. However, the very fact that there's no profit incentive to research these diseases makes them perfect candidates for open source style research; there's no profit incentive to keep secrets either.

By Ginger Taylor (TSL Founder)

Technorati Tags: biology, open-source, The synaptic leap

hello

2006-02-13T12:06:00.000-08:00

Hi all!

This is a new blog I am starting to narrate the adventures of developing a open-source initiative for biomedical research. I plan to extend that blog until the development is done, and I hope this will be over a year work. So that is why I name this a "year journey to open-research".

We are actually doing that within The Tropical Disease Initiative and in collaboration withe The Synaptic Leap people. I will be updating you with the ups-and-downs of such a experience. Hope that it will be informative to all.

To start with, you can read what Jamais Cascio thinks about our initiatives:

TSL@ here
TDI @ here

All the best,
Marc

Technorati Tags: biology, open-source