Suggested Changes to F@h Website

[Jesse_V]

Are there any plans on updating the FAQs and Disease Research pages to reflect the changes in scientific consensus? For example, the paragraph on Osteogenesis Imperfecta dates back to Nov 9th 2003 (source) and I haven't run across any "OI leads to miscarriages" statement on Wikipedia or the few scientific papers I've browsed. Maybe I haven't looked hard enough. I suspect that there have been a lot of changes in scientific findings related to the disease. I was just wondering if there any plans on rechecking the facts. Would be a shame if the PG gave the impression there that they were pursuing something that's been rendered obsolete. There are several other paragraphs which are equally old (like a copy/paste from the old Genome@home website). Is there any way that I could assist with the updating or something? Are such changes covered in the upcoming website overhaul? I think updating could be performed while still keeping things simple for regular people.

[bruce]

The FAH website doesn't report all information related to a specific disease, only those results that are based on FAH simulations. Thus scientific papers published by FAH researchers are listed when a paper is accepted for publication (equivalent to "... which advance science"). A significant part of any scientist's responsibility is to stay up-to-date on all advances in their field, which means they have to read everybody else's research. Whether they made a specific discovery or somebody else did, scientific advancement builds on previous knowledge and suggests areas for new studies.

Researching ALL publications that are related to a specific disease is beyond the scope of the FAH website.

[Jesse_V]

The FAH website doesn't report all information related to a specific disease, only those results that are based on FAH simulations. Thus scientific papers published by FAH researchers are listed when a paper is accepted for publication (equivalent to "... which advance science"). A significant part of any scientist's responsibility is to stay up-to-date on all advances in their field, which means they have to read everybody else's research. Whether they made a specific discovery or somebody else did, scientific advancement builds on previous knowledge and suggests areas for new studies.

Researching ALL publications that are related to a specific disease is beyond the scope of the FAH website.

I understand that. It would be a long page indeed if it brought in all scientific publications on the disease. But there are many review articles which seek to illustrate current scientific consensus without going into complex detail. Since I've discovered how old some of the passages are, (not just on the Diseases FAQ page) I just wanted to make sure that they still hold true. Given the scope of Folding@home and the size of its userbase, I feel that it's important that things stay up-to-date. With my limited understanding of the molecular mechanisms behind each disease, its difficult for me to identify specific problems though.

[Jesse_V]

Neither of the two provided links to paper #49 ("Automatic State Decomposition Algorithm") work. 404 Errors.
I tried to find an alternative link using Google Scholar, but wasn't able to find it. After Googling parts of the abstract, I believe that the actual title is "Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics" Here are possible alternative links:
http://jcp.aip.org/resource/1/jcpsa6/v1 ... p155101_s1
http://jcp.aip.org/resource/1/jcpsa6/v1 ... w=fulltext
http://scitation.aip.org/getpdf/servlet ... rog=normal
But I'm not sure which ones will actually work for most everyone since I'm on a university network. Choose at will.

[ArVee]

First link works, other two require log-ins. Just advising from outside the university network.

[7im]

Neither of the two provided links to paper #49 ("Automatic State Decomposition Algorithm") work. 404 Errors.
I tried to find an alternative link using Google Scholar, but wasn't able to find it. After Googling parts of the abstract, I believe that the actual title is "Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics" Here are possible alternative links:
http://jcp.aip.org/resource/1/jcpsa6/v1 ... p155101_s1
http://jcp.aip.org/resource/1/jcpsa6/v1 ... w=fulltext
http://scitation.aip.org/getpdf/servlet ... rog=normal
But I'm not sure which ones will actually work for most everyone since I'm on a university network. Choose at will.

Used first link to fix.

[Jesse_V]

Neither of the two provided links to paper #49 ("Automatic State Decomposition Algorithm") work. 404 Errors.
I tried to find an alternative link using Google Scholar, but wasn't able to find it. After Googling parts of the abstract, I believe that the actual title is "Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics" Here are possible alternative links:
http://jcp.aip.org/resource/1/jcpsa6/v1 ... p155101_s1
http://jcp.aip.org/resource/1/jcpsa6/v1 ... w=fulltext
http://scitation.aip.org/getpdf/servlet ... rog=normal
But I'm not sure which ones will actually work for most everyone since I'm on a university network. Choose at will.

Used first link to fix.

Thanks very much! Could you please change its title too, since AFAIK all the other papers on the page reflect the actual name of the publication? Or is there a particular reason that "Automatic State Decomposition Algorithm" is preferred to "Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics"? I would guess simplicity, but then again we have publications named things like "Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration."

On the upside, well done Dr. Pande for taking the time this morning to improve http://folding.stanford.edu/English/Learn, it looks much better!
Overall I'm very pleased with all the website changes, I think the simplicity and organization is very helpful to all.

[VijayPande]

On the upside, well done Dr. Pande for taking the time this morning to improve http://folding.stanford.edu/English/Learn, it looks much better!
Overall I'm very pleased with all the website changes, I think the simplicity and organization is very helpful to all.

Glad to hear it. We've been trying to streamline the site to make it easier to use and more aesthetically appealing.

[Jonazz]

Has the diseases page disappeared? I liked that page, it gives a short summary what the link with F@H and the particular disease is, and what advances have been made. COuld you consider bringing it back?

[Jesse_V]

Has the diseases page disappeared? I liked that page, it gives a short summary what the link with F@H and the particular disease is, and what advances have been made. COuld you consider bringing it back?

Still here: http://folding.stanford.edu/English/FAQ-Diseases
From the main site, it's "Learn"->"Frequently Asked Questions"->"Diseases studied FAQ"
There's also a link to the Disease FAQ from the bottom of the "Science behind Folding@home" page

[7im]

We could probably bring that page up to the learn page.

[Jesse_V]

We could probably bring that page up to the learn page.

Good idea. How about a "Diseases we are studying" link under "Why to Fold"?

[Jesse_V]

Also, the latest publication can go on Dr. Pande's page: http://folding.stanford.edu/Pande/VijayPandeCV
Following the format of the other publications, I believe the citation should be:

194. P. A. Novick, D. H. Lopes, K. M. Branson, A. Esteras-Chopo, I. A. Graef, G. Bitan, V. S. Pande. Design of β-Amyloid Aggregation Inhibitors from a Predicted Structural Motif. Journal of Medical Chemistry, in press (2012).

You may also want to check up on the "In press" status of some of those recent publications. Some of them may have actually been moved from accepted for publication to actually being published. I'm not sure how to check them myself though.
With nearly 200 publications to his name, (assuming that list is all of them) I'm hereby defining the term "Pande number". Those who co-author with Dr. Pande (e.g. Dr. Kasson) have a Pande Number of 1, those who co-author with them and not Dr. Pande have a value of 2, and so on. Pretty impressive!

[Jonazz]

Has the diseases page disappeared? I liked that page, it gives a short summary what the link with F@H and the particular disease is, and what advances have been made. COuld you consider bringing it back?

Still here: http://folding.stanford.edu/English/FAQ-Diseases
From the main site, it's "Learn"->"Frequently Asked Questions"->"Diseases studied FAQ"
There's also a link to the Disease FAQ from the bottom of the "Science behind Folding@home" page

Thanks!

[Jesse_V]

Has the diseases page disappeared? I liked that page, it gives a short summary what the link with F@H and the particular disease is, and what advances have been made. COuld you consider bringing it back?

Still here: http://folding.stanford.edu/English/FAQ-Diseases
From the main site, it's "Learn"->"Frequently Asked Questions"->"Diseases studied FAQ"
There's also a link to the Disease FAQ from the bottom of the "Science behind Folding@home" page

Thanks!

No problem. I see 7im went and put a direct link to it from the Learn page, which was a really good move.