Well Sourceforge/software development is certainly applicable to the development of tools for bioinformatics purposes, but bioinformatics hasn’t really solved any problems as it relates to disease, there still is a wet lab component. So the question remains how does drug development occur in a virtual environment. Let’s say I had just done a clustering algorithm on phylogenetic profiles across 82 genomes. I had the clustering data, I had my experiment algorithm and method but now I need help in deciding what and how to both store that information in a meaningful way and then access additional information that in combination with my results could be useful. So let’s say we wanted to focus on a particular tropical disease and it is commonly known the series of genes, both regulating and protein coding. How do we collaborate further to design a drug?

-Will

-----Original Message----- From: Jacob Lester [mailto:jacob.lester@fdisolutions.com] Sent: Wednesday, February 16, 2005 11:49 AM To: 'Will Rosellini'; tdi-discuss@tropicaldisease.org Subject: RE: [TDI-discuss] (no subject)

My background is software development and I have worke on many occasions with other software developers around the world on one project. Source control and management

for such projects is well documented and there are tools to aid this. SourceForge is a good example.

Could you elaborate on the problems encountered by Cambia?

Regards,

Jake

-----Original Message----- From: tdi-discuss-bounces@salilab.org [mailto:tdi-discuss-bounces@salilab.org]On Behalf Of Will Rosellini Sent: 16 February 2005 16:33 To: tdi-discuss@tropicaldisease.org Subject: [TDI-discuss] (no subject)

So does anyone here have experience in virtual software development, open source development etc...seems like the TDI needs a plethora of bioinformatics people who can come up with a technical framework to allow contributions from people across the globe. The Open Source Biology project, Cambia's is trying but they are running into the same troubles.

Does anyone know of projects, other than software development that have occurred entirely virtually?

-Will

http://xpostmail.com/461a08f63e6a11f5e0d98f2d20529fc2worker.jpg

http://xpostmail.com/da74edb7cd19693dbc5d94d0d55b9ad8worker.jpg

The wetlab side of things would be best done in collaboration with Universities or other organisations (NGO's, Corps etc.) that have a shared interest in developing the drugs. For example, in the U.K. I know there are several organisations that will fund projects like TDI or offshoots of TDI e.g. http://www.rcuk.ac.uk/escience/ one of the criteria is that a university is a partner, I believe the universities can be anywhere in the EU. There is no reason why the university could not provide wet lab facilities while the bioinformatics and other software tools and research could not be done by the rest of the TDI community. Failing that 3rd party sponsorship could enable such facilities to be rented.

With regards to storing data, if there are no suitable XML schemas for holding structured data it is not too tricky to devise one that can be used by most of the community. Any data that is unstructured or unsuitable for storage in a well-defined XML schema then using tools such as Lucene could index the data and make it readily searchable. Most of these issues have been addressed by other projects already and the solutions are well documented.

Regards, Jake

-----Original Message----- From: tdi-discuss-bounces@salilab.org [mailto:tdi-discuss-bounces@salilab.org]On Behalf Of Will Rosellini Sent: 16 February 2005 16:58 To: tdi-discuss@tropicaldisease.org Subject: RE: [TDI-discuss] let's talk about the barriers

Well Sourceforge/software development is certainly applicable to the development of tools for bioinformatics purposes, but bioinformatics hasn't really solved any problems as it relates to disease, there still is a wet lab component. So the question remains how does drug development occur in a virtual environment. Let's say I had just done a clustering algorithm on phylogenetic profiles across 82 genomes. I had the clustering data, I had my experiment algorithm and method but now I need help in deciding what and how to both store that information in a meaningful way and then access additional information that in combination with my results could be useful. So let's say we wanted to focus on a particular tropical disease and it is commonly known the series of genes, both regulating and protein coding. How do we collaborate further to design a drug?

-Will

-----Original Message----- From: Jacob Lester [mailto:jacob.lester@fdisolutions.com] Sent: Wednesday, February 16, 2005 11:49 AM To: 'Will Rosellini'; tdi-discuss@tropicaldisease.org Subject: RE: [TDI-discuss] (no subject)

My background is software development and I have worke on many occasions with other software developers around the world on one project. Source control and management

for such projects is well documented and there are tools to aid this. SourceForge is a good example.

Could you elaborate on the problems encountered by Cambia?

Regards,

Jake

-----Original Message----- From: tdi-discuss-bounces@salilab.org [mailto:tdi-discuss-bounces@salilab.org]On Behalf Of Will Rosellini Sent: 16 February 2005 16:33 To: tdi-discuss@tropicaldisease.org Subject: [TDI-discuss] (no subject)

So does anyone here have experience in virtual software development, open source development etc...seems like the TDI needs a plethora of bioinformatics people who can come up with a technical framework to allow contributions from people across the globe. The Open Source Biology project, Cambia's is trying but they are running into the same troubles.

Does anyone know of projects, other than software development that have occurred entirely virtually?

-Will