Hi, Rosetta@home community!

I just joined the Baker lab as a new postdoc, and I'll be spending part of my time developing materials to help participants understand the science behind Rosetta@home -- what it does, why it does it, and how the research relates to chemistry, biology, and medicine.

Here's what I need from you:

1. Questions! What do you wish you knew about Rosetta@home? What things are hard to understand, or badly explained?

2. How would like to learn about it -- writen explanations, info-graphics and pictures, video, interactive "games" and graphics, or something else?

3. What resources have you already used to help understand R@H? What did you like and dislike about them? (I'm going to be creating some new materials, but I also hope to take advantage of some of the great science resources already on the web.)

4. I would love help with this project! If you would be interested in helping, what would you like to contribute? Should there be a R@H wiki (like Wikipedia) or just submit contributions by email?

Be patient with me as I get up to speed in the lab, but I'm really looking forward to contributing to the Rosetta@home community!

Best,
Ian

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I've really never understood exactly what the random starting value does. Is it essentially a hash of all the amino acid orientations? Or does it lock two specific AAs into one specific orientation for the model? Or what?

I think that narrated animations such as Laura has done will work well.

One thing I dislike about the materials I've seen to date is that there isn't any kind of rating scale for the technical level of the materials. So you have to go look before you realize it is beyond the level my scientific understanding allows me to comprehend. Some are obviously intended for a novice and some intended for a PhD, but no indication beforehand as to which you are about to get in to.

One area of confusion has been all of the various fields of study and methods that are under investigation in BakerLab. There is abinitio, docking, symmetric; there is robetta, Rosetta@home, BakerLab's own Linux cluster; AIDS research, cancer, Alzheimer's, CO2 removal. It is often difficult to connect the dots and distinguish between these various facets.

Also some description of other organizations and scientific areas that Dr. Baker and team are collaborating with would help us to see how the vast area of medical science research pieces fit together. A chart showing the various entities and a narrative of how you could go about getting from point A, a person with a disease, to B, disease identification, to C, docking experiments, to D, designed drug candiate, to E, drug trials would really be helpful. Perhaps use the AIDS research as a frame of reference. Seeing the whole picture would help understand where BakerLab fits in to the study of AIDS. Often people ask how close Rosetta@home is to finding a cure. Seeing where BakerLab fits in to the bigger scheme would help people see why that is not exactly what they are working on. ...and why their research is important anyway.

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Add this signature to your EMail:
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/

First you should explain things on a 8th or 9th Grade level. The jargon is really irritating. Most of the participants are not Biochemists. So the minute jargon is used most of your audience gets quickly lost.

If this is even possible: Try to explain in a step by step fashion what rosseta is really doing or trying to do. I have been doing this project for 2 years and all this time I thought I was helping develope a program to crack the folding problem (whatever that is). Now I am not sure what is going on.

Most people what to know about PROGRESS. How much better or different is rosseta after 2 years of distributed computing. This would explain alot to many folks.

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As feet1st said in the post before, there's confusion with the diseases studied. Here are a few points I'd like you to focus on ( in order of importance, 1. being the most important):

1. Is the disease related research terminated or still going on? That question should be covered in the first place. A subpage, with a list of the diseases covered and a short progress message (1 sentence is enough) on the current stage of the research (planned, ongoing, terminated, results published, ...)
This type of progress report encourages many people to keep on supporting the project at WorldCommunityGrid and Einstein.

2. The WU description should be updated more frequently (at least once a month, once every second week is ok too)

3. A newsletter could be sent to all the accounts (as SETI did) to wake up old participants and to encourage others to restart crunching rosetta. This newsletter has often been discussed among the active forumers, it should include a brief summary (otherwise nobody will read it) of the science done so far, like the HIV research.

I greatly appreciate your initiative Ian Davis, I hope some of my points can become reality :).

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I think that a very important thing is not only what information is available, but how it is presented.

If Rosetta wants to be friendly to newbies and non-technical users, I think it should redesign its frontpage and take the Apple/Google approach.

f.ex. The first page the user sees could be three big icons. One is "Learn about Rosetta@Home", the next one is "Install Rosetta@Home on your computer" and the third one is "Advanced Features for existing users".

The first one can be a clean FAQ with big fonts. Answer all the typical questions, give a list of things currently in progress, etc.

Second one explains very clearly how to install the software and get started.

And the third one takes you to a place that looks like the current Rosetta frontpage, with tons of options and info.

The problem is that currently a new user comes and sees about 50 things on the frontpage and leaves. It's unnecessary friction for newbies, they don't need to see all that at first.

Thoughts?

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An explanation of what the names of the various projects mean in plain english.

What is Cntrl01ABRELAX mean in a simple form?
Where can we find information or can Baker Labs explain the various proteins being studied? If you look at the current work units in progress for CNTRL01 you see all kinds of letter number combos and then filters. So what are we filtering?

Some simple explanation of what we see when we go look at the results and the result plots would be nice. What is a decoy? What is a starting unit? In the plots the red dots represent our findings. But when you zoom in, what are you "zooming"?

A laymans explanation over what we see when we display the graphics screen.

A "users manual" as such, over the different features of BOINC/Rosetta and how to customize them to the most common settings. For instance, what would be a good run time per work unit? 4hrs or 6hrs or what? Why the difference between requested credit and granted credit. (we have had some long discussions on number crunching on this and how work units function with certain CPU's)

Some information on how WU's are assigned to computers depending on whether they are super crunchers or putters like mine with a AMD 2800+

Maybe a nice page on who's who over there at Baker Labs and what they do for the project. Maybe a email addy or web page section to send Rosetta system issues to, such as WU's not being sent out, or the validator being offline. We post often in the problems threat of number crunching about these issues and then it can go on for a couple of days before we see a solution to the problem or any sort of information about what the problem is/was.

I have to agree with point 2 of Tom. It would be nice to have that section updated more often. Its kind of something that someone gets around to once in a great blue moon.

A monthly newsletter would be nice to see, either on the webpage or mailed out to people, telling us how things are going with the projects, what new projects are coming in the future and other general news about the project.

Those are some things that come to my mind.
Nice to see someone looking into making RAH more general user friendly.
You certainly have a big project on your hands and I wish you lots of success in completing it.

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My doctorate is not in either Biology or Chemistry.....

In a general, high-level, presentation, I am interested in CASP. Maybe a few simple bar graphs and charts...

During CASP7, I stopped crunching other projects, and crunched Rosetta almost exclusively.

This was the "peer olympics".

I am aware that there are some previous threads and even the CASP website. But either I am not finding the correct information, or not properly understanding the information that is being presented.

What was the total number of Targets in CASP7?
How many Targets was Baker Labs ("BL") able to submit?
If BL was not able to submit on all Targets, why (time, not enough tflops)?
On how many Targets did BL perform "very well" (whatever that means)?
Why?
Why is/isn't this level of performance "good enough"?
On how many Targets did BL perform "poorly" (whatever that means)?
Why?
What was BL able to learn from other participants and how they performed?
Overall, out of x participants, where did BL rank?
What refinements / changes have been made to Rosetta as a result of CASP7?
What preparations are being made for CASP8 (time, tflops, etc.)?

Ian's gonna ask me to lock the thread if this keeps up! :)
Just kidding... great input. Keep it coming.

Bad Penguin brought up CASP. It would be good to discuss and develop material to explain CASP, that way the material is all ready when the lab is gearing up for the next CASP. It would also be very interesting to understand all of the work that the Baker team is doing with the BOINC results in order to prepare a submission. I get the sense that they have to manually review a given target and make some broad determination as to what approach will be most effective in solving it (jumping, abinitio, barcode)... how do they make such a determination? And then of course you have to explain what each of those approaches means.

This thread seems to be quickly turning in to a "suggestions on how to improve Rosetta@home" (especially the website). That subject is too broad, and doesn't sound like what Ian took on.

Please review the thread subject line and try to focus on what you know, or wish you knew about the science.
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Rosetta Moderator: Mod.Sense

4. I would love help with this project! If you would be interested in helping, what would you like to contribute? Should there be a R@H wiki (like Wikipedia) or just submit contributions by email?

First of all I'd be glad to help you. I thought about the idea of a wiki (I contributed in one before), however I think it will be hard for new members to get the information they want in such a complex organisation. For instance if they type "rosetta error" in the search engine, they don't necessarily find the information they're looking for due to the very simplified language. (Encyclopedia: the reader knows a complex word and wants and explanation/more info).

In this case it's the opposite. That's why I found this way of putting it more basic: http://boincfaq.mundayweb.com/index.php

This thread seems to be quickly turning in to a "suggestions on how to improve Rosetta@home" (especially the website). That subject is too broad, and doesn't sound like what Ian took on.

I hope this doesn't imply that there won't be any improvements to the website :D

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Wow, great discussion! Let me try to respond to a few general points, and then a few specific things:

1. Relevance to medicine/health. This seems to be the most important issue to most folks -- seing how what they're doing with R@H is going to help cure cancer/AIDS/Alzheimers. I want to make sure we're enthusiastic while remaining honest. You can't say the Wright Brother's single-handledly enabled your trans-Atlantic vacation, but you can say their contribution was vital :) So it is with R@H. I think clarifying #3 below would help a lot with this too.

2. Appropriate level for materials. 9th grade level isn't so far off -- many people don't have much if any science after high school, and probably forget a lot of what they knew. It also plays well with the other face of my project, which is to do science outreach to high school kids via Rosetta. Demand for more advanced materials seems to be either about specific projects now in progress, or technical facets about computing power etc.

3. Diversity of projects. The Baker lab works on a *lot* of things -- there were 30+ people at group meeting yesterday, and they all have their own research projects. That's why it seems like Rosetta does so many different things. They *are* all connected, it's just hard to see unless you're very familiar with the field. I agree that some overview of what all Rosetta@home works on would be useful.

4. Communication with users. I hear that people want to know more about what their computers are doing at any given moment, and more (understandable) info from the screen saver. I know a little work is being done on the screen saver at least, so I'll mention it, but it is outside my domain.

5. Previous threads. I know there have to be other great threads from the past with explanations you found helpful. If we could organize some of them by topic that might help answer some of the higher-level questions about Rosetta itself. Post links to your favorites?

And now the specific things:

Feet1st, thanks for the link to Laura's thread. Some great ideas in there too.

greg_be, thank you for the suggestions. Many sound quite good, though as Mod.Sense point out, some may be beyond my scope.

The_Bad_Penguin, your questions are good ones, but more technical than the level I had been thinking of addressing. The CASP competitions are always discussed extensively in the scientific literature -- I think there's usually a special issue of some journal devoted to each one, the results, how different labs performed. Would that be an appropriate place to direct you?

Tom P, I like that list. I'm definitely envisioning something structured, not free-form, I just wondered if a collaborative model could be used to create it. The more I think about it, though, the more I think not.

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i think i may have mentioned it in my first post, but on proteins (the letter number combo in the work units), maybe there could be a place or a 'encyclopedia' as such about what each of these proteins do, or what they are related to disease wise. I know we have been pointed to a website that talks about these, but I keep losing the web addy and it would be nice to have a laymans written page about them.

Of interest is the 1gidA RNA work unit, which we had trouble crunching in a previous version of RAH, so that peaked my interest.

Perhaps you could write something up as to what BL is interested in doing with the information from the RNA work units. How does studying RNA improve what BL has set out to do as their mission? Also some simple stuff on DNA, RNA, how they interact, how modifying one or the other with what is being seen here changes the way a certain disease as such behaves genetically. (hope that makes sense)

Also hom001, what is that?

I also have a interest in what WU's relate to cancer. As I put in my profile my Mother in law is fighting cancer. So thats the reason I joined in on this project. How does the work BL does affect the way doctors will be able to treat/diagnose cancer in the future?

Hope this stuff is a little more in your scope. I see we got carried away on how to improve and not the science part of things. Hope you can pass the improve stuff along to someone who deals with that.

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Here's some information about the 1gid protein: http://www.rcsb.org/pdb/explore/explore.do?structureId=1GID

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The active work units log tells what a given protein is. As previously noted it is not presently always up to date.

But I think the main point is that the description there for 1gid of "The P4-P6 domain from the self-splicing Tetrahymena group I ribozyme" doesn't tell me why BakerLab finds this protein interesting, and why they are sending out tasks based on this protein. If there were a picture of the known native structure and a little red circle around a funny little loop in it with notes that "we are trying to understand how to predict that the backbone would take this odd formation at this point" then I could feel I "understand" what I'm crunching. Even if I do not understand why this little loop was unusual or difficult to predict.

If I am running a BARCODEd task and someone posted the AA sequence with the subgroups of AAs highlighted and explained that these portions of the conformation are considered to be already defined and known, and fixed in the model, that would help me grasp a bit more about how they go about deciding to barcode some of the CASP proteins of unknown structure. And it might help me to better see why we have JUMPING tasks. And, most importantly, it would help people see that we aren't jumping around randomly. There is intelligence behind the process.

So far as threads I've learned about the science in... most are summarized in the Project Information Index thread here.

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Add this signature to your EMail:
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/

One area of confusion has been all of the various fields of study and methods that are under investigation in BakerLab. There is abinitio, docking, symmetric; there is robetta, Rosetta@home, BakerLab's own Linux cluster; AIDS research, cancer, Alzheimer's, CO2 removal. It is often difficult to connect the dots and distinguish between these various facets.

In response to, How are all the things the Baker lab works on related? The lab does work on a huge variety of topics. What connects them is computational modeling of protein structures: all the projects require, in some way, that we use a computer to predict what shape a protein will have and/or how it will interact in a given situation (without doing "wet" experiments -- though we often test our predictions afterwards in the real world).

Also some description of other organizations and scientific areas that Dr. Baker and team are collaborating with would help us to see how the vast area of medical science research pieces fit together. A chart showing the various entities and a narrative of how you could go about getting from point A, a person with a disease, to B, disease identification, to C, docking experiments, to D, designed drug candiate, to E, drug trials would really be helpful. Perhaps use the AIDS research as a frame of reference. Seeing the whole picture would help understand where BakerLab fits in to the study of AIDS. Often people ask how close Rosetta@home is to finding a cure. Seeing where BakerLab fits in to the bigger scheme would help people see why that is not exactly what they are working on. ...and why their research is important anyway.

In response to, How does Rosetta@home research lead to cures for diseases? Proteins are involved in performing almost everything that goes on in your body. Diseases usually result from some breakdown in the system -- cancer can be caused by out-of-control signaling proteins, HIV proteins attack our immune system, and Alzheimer's is thought to be caused by damaged proteins building up in clumps in the brain. So the Baker lab is interested in developing techniques to (1) understand these processes more quickly or cheaply (e.g. structure prediction, docking) and (2) invent proteins or drugs that can fix some of these bodily processes when they start to go wrong.

Here's my attempt at a narrative: suppose I go the doctor's office for my annual checkup some years down the road. He draws a little blood and sends it to the lab, where it's tested with special sensor proteins that were designed using Rosetta. These sensors report on mundane things, like how much glucose is in my blood (i.e., am I diabetic?), and special things, like whether there are any molecules that are known signals for cancer. This could be very fast: 10 minutes later my doctor returns and says most things look good, but I probably have an early stage cancer. Other tests, MRIs, etc. confirm I have a small tumor: not good. But exquisitely sensitive designed sensor proteins (Rosetta again) are used in a few more tests, and they can tell it's a specific subtype that is known to be caused by a specific malfunctioning protein. (It took other researchers in other labs years to work that out, of course, using a wide variety of techniques.) Although no one has every determined the structure of this protein directly, they didn't have to, because Rosetta was used to predict its structure with very high accuracy. That prediction was so accurate that Rosetta could also be used to predict what sorts of molecules might bind to it and stop it from causing problems, leading to the development a drug that effectively cures my cancer. Of course, chemists at a pharmaceutical company had to work out how to manufacture the drug efficiently, and doctors and nurses did years of clinical trials to make sure it was safe and effective.

Does this help at all?

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Is the disease related research terminated or still going on? That question should be covered in the first place. A subpage, with a list of the diseases covered and a short progress message (1 sentence is enough) on the current stage of the research (planned, ongoing, terminated, results published, ...)
This type of progress report encourages many people to keep on supporting the project at WorldCommunityGrid and Einstein.

Just to be explicit, yes, disease-related research is still going on. The summary on the front page is the best source *I* know of right now for what diseases are currently being targeted. But the most important thing is that as Rosetta improves, it will become possible to target all disease in a much more precise way, leading to more effective treatments and fewer side effects, because we're not thrashing around in the dark. In the long run, I think projects like this will revolutionize medicine, but it's important to realize that it will unfold over a period of years and decades -- we're not walking down the hall to inject Rosetta in a sick patient :)

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These are a great start Ian.

"we're not walking down the hall to inject Rosetta in a sick patient"... but understanding where we are and how we proceed from here, "how do we know when we're 'done'?" is a common question.

The narrative is good. It might be even more clear if you project into the future again and illustrait how we go about developing a cure and/or vaccine for bird flu. And how we do so BEFORE it mutates in to something that infects humans. And an animation of how a cancer cure would look as it works would be very cool.

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Add this signature to your EMail:
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/

Wow, I'm impressed, this is the best post I read on the forums since Dr. Baker's last journal entry.

This has to be put on a subpage of the frontpage as soon as possible before it submerges.

I like the narrative, it only needs to be spiced up by a proper, clear form (like numbering the different steps, using symbols like => to show a consequence...)

The 2 questions you focused on seem clear to me, ready for a FAQ.

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love the narrative and feet1st's idea.
thats about the best explanation i've seen around in some time.

on a subnote about front page and targeted disease's summary,
it would be nice to read where baker labs is at in its research with the disease's listed on the front page and again what work units correspond with the each disease.

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Here's a 5min attempt at a possible progress report subpage:
Click here

Do you think this could be useful?

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A collection of links for you, many of which have other useful links in the course of the discussion.

Some attempts at how you might keep kids interested long enough to hear what you have to say and how to explain Rosetta:How Rosetta works, an explaination your cat will follow

My attempt to bring in some feedback from young people that are running Rosetta: here

We tried to put together an EMail to use for folks to explain the project to their friends in an effort to bring in more participation in the project
http://www.geocities.com/feet1st/TellAFriend.html

We also put together the letter to inactive Rosetta crunchers to try and retain crunchers. I guess this is the final copy.

Another thread tries to pinpoint the "simple" explaination.

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Add this signature to your EMail:
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/