Hi to everyone,
I would like to ask the community if they think a project which focuses on the Cystic-Fibrosis geneprotein model could be added the exisiting programme of work undetaken by BOincRosetta ?

Secondly (with credit to David Baker) for the existing programme, would the community favor a say in what computational models are available to run on their resources, perhaps taking a vote on proposed projects ?

For myself, I would prefer running computational models e.g. on Cystic Fibrosis which add to the "immediacy" of current research, and at the same time could open up areas of potential breakthrough not yet realised.

best regards to all,

Derek Conlon
www.dnarna.info

I got into this project for cancer related studies, but I am willing to use my computer to crunch anything that will help a person in the future.

CF has never been an issue in any of my relatives, but back in my junior/high school years I use to try to raise money for CF from people on my paper route. That is to far back to remember who or what organization was involved in this but I do remember the name CF to be the reason we were trying to raise money.

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i can see why it would appeal to some people to be able to pick exactly what jobs their computers were running, but then if one person decides to take more of one type of job it just means that other people are more likely to get the other jobs - they're all going to get crunched at some point - so there is no net effect on the results as it's down to the lab what goes in the queue.

HTH
Danny

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Derek, I believe you are asking if others would like the choice of what specific diseases they would like to devote their PC time to. This is an option they have on the World Community Grid. With Rosetta, you are primarily helping to improve the basic protein tooling used by researchers all over the world in their work on specific diseases. Rosetta@home does comparitively little research on specific diseases. They are working to develop the tools that are needed to develop cures to specific diseases in the future.

Take Cystic Fibrosis as an example. It is caused by a genetic mutation. Some day scientists will be able to FIX such flawed genes. The way they will likely do that is to create a virus which locks in to the area of the cell's DNA that is flawed, and replace it with the corrected DNA. The current problem is, knowing how to create the virus with the corrective gene sequence, and how to get it to specifically target the correct location on the DNA. Rosetta is primarily focused on developing that underlaying technology needed to do such a thing. Then other scientific teams will apply that knowledge and technology to Cystic Fibrosis and other genetic diseases.

Before we're likely to see such a DNA correction, we're more likely to see Rosetta technology used to create vaccines to viral infections. Bird Flu is in all the newspapers these days. Such viruses are all around us and constantly changing. Why wasn't bird flu in the news in the 1960s? Because it didn't exist at that time in the form it now has. Mutations of viruses occur over time and new strains come around.

Rosetta is working on the technology that will allow researchers to take a specific virus like bird flu, and create a specific vaccine for it, and to do so before such a disease spreads around the world and infects millions of people.

So I hope you will agree with me that Rosetta's research is of key importance to the human race. And that the project is worth supporting, even if they don't presently do research on a specific given disease.

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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

Well it would be nice to have research in all compatible areas that the Rossetta code will work for. It would also be nice to opt in/out of different types of research.
For instance we could have tick boxes in the preferences for
1) Methodology (i.e. improving the code and test areas)
2) HIV
3) Alzheimers
4) whatever comes along....
5) Beta testing.

..

We had a similar thing at Find-a-Drug where you could opt in and out of specific types of research. It keeps people happy. Some people are dedicated HIV crunchers, some cancer and some go for respiratory. Some don't liek the methodology part, though for this project it needs to be fixed at always on, but run as second priority (option). This makes the people feel better especially if areas people don't believe in or are unsure about can be opted out of.
Maybe as areas expand this can happen...

As for voting for what should be run, you already can. You eiter run it or don't. Quite simple ;-)
We are helping speed up the research for what the Rosetta people wish to study, not what we wish to study. Of course if you have a proposal you could always contact the D. Baker and see what he says...

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Team mauisun.org

Derek: One of the difficulties we had at FAD (Find-A-Drug) was finding labs that would test out the results we came up with. For CF, we'd need knowledge about CF that would benefit from something like the HIV vaccine therapy that the Baker Labs is working on - or information about which receptors to block so CF symptoms are stopped.

Once there's something to work with, then Rosetta can be used - either here, at World Community Grid (which is using an older version of Rosetta for at least one of the projects they're running) or a new Boinc project - perhaps CF only.

After years spent on DC projects, I'm still waiting for something we've worked on to make it onto the market as a cure/treatment. It takes time; and perhaps the current work by Bakerlabs on HIV vaccines will be the first DC medical project to make it out into the real world and encourage more DC medical breakthroughs.

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Derek: One of the difficulties we had at FAD (Find-A-Drug) was finding labs that would test out the results we came up with. For CF, we'd need knowledge about CF that would benefit from something like the HIV vaccine therapy that the Baker Labs is working on - or information about which receptors to block so CF symptoms are stopped.

Once there's something to work with, then Rosetta can be used - either here, at World Community Grid (which is using an older version of Rosetta for at least one of the projects they're running) or a new Boinc project - perhaps CF only.

After years spent on DC projects, I'm still waiting for something we've worked on to make it onto the market as a cure/treatment. It takes time; and perhaps the current work by Bakerlabs on HIV vaccines will be the first DC medical project to make it out into the real world and encourage more DC medical breakthroughs.

This is an important point. To get all the way to a therapy or drug to cure a disease is a very big effort that requires efforts at many levels. In our HIV vaccine design work, we are working closely with some of the leading groups in the world who have many years of experience in evaluating potential vaccines and testing them, and the Gates foundation is committed to bringing any vaccines we or others involved in the project design into actual use. Similarly, in our work on enzymes that would destroy the parasite causing Malaria, we are collaborating with experts in insect population genetics and other areas necessary for really getting something to work. In our work on developing reagents for curing cancers and other diseases caused by mutations in human cells, we are working with people who are experts on these diseases and have experience with the complications of gene therapy.

I think we definitely could have a list of proteins that all of you could prioritize that we could start building models for. But without collaborators who would work to develop drugs based on these models it is not certain that this modeling would contribute to developing cures (it is possible though).
But I am certainly open to this possibility if many of you are enthusiastic about it.

The calculations we have planned for the next 6 months on rosetta@home are a mix of research directly aimed at one of the goals mentioned in the above paragraph and other medical applications, and tests aimed at improving the fundamental algorithms underlying all of these efforts. This second area--methods development--is really important as many of you recognize because computational methods are still far from perfect; with the help of rosetta@home we are making rapid progress improving the methods, and the better they become the more powerful tools they will be for fighting disease.

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