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Dejan:
If there's questions about what's said in Dr. David Baker's daily journal, please post them in the "Discussion of Rosetta@Home Journal" so that they can be answered. Some of the participants of Rosetta are familiar with various aspects of the science involved, and can do a good job explaining what those biological or chemistry related phrases refer to - in language that we non-biochem-majors can understand. So even if the descriptions by David Baker aren't easily understood, ask again and a few of the other participants will share an explanation that you, I, and the rest of the readers with that question can understand.

The Casp targets were of unknown structure; although if you visit the CASP7 site, you should be able to get a description of what each of the targets was, and with the actual name of the target t0316, you can find out where that protein came from, and what it's purpose is. In one of the discussions about the proteins that we were working with, there were links to help look up more information on all the proteins we deal with. There is a thread with descriptions of the proteins we're working with that was being updated regularly prior to CASP for those that wanted to find out that the strange 4 or 5 letter designation was some compound from a chicken. (An example of the only protein I looked up..)

Keep in mind that prior to the HIV WUs that we're getting, we've been working with known proteins (except for the CASP targets) to test the Rosetta client and improve it so that we could use the Rosetta client for applied research such as the HIV WUs.

So most of what you're asking for - are issues that have been dealt with in the past. As we pick up activity, it'll be time to make them more prominent.

Perhaps someone will share the links to the protein lookup discussion.

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Dejan, welcome to Rosetta!

Great thoughts there. I'll just bold your idea here:
Create & illustrait project milestones.

In fact the idea has come up before. So it is good to revisit it and see if something can be devised to meet this objective.

Many of us have a hard time understanding Dr. Baker :) Some among us (not I) do have bio and chemistry/physics backgrounds, and they have been very helpful in answering questions.

We all work together to translate Dr. Baker in the journal discussion thread. You can post specific questions there, but I do realize your point is basically that you've got so many questions that it is hard to know where to start.

And while "most participants" don't even read the boards, I do agree that there's something about that thermometer colored in with red when the United Way fund drive is underway that gives a quick and simple sense that something has been accomplished.

I believe that the Bakerlab is actually working to various degrees on numerous projects and objectives at the same time. So, perhaps they'd need more then one progress bar.

I might summarize the idea this way... take the things you plan to do over the next 12 months or so and write them all down, and stick some target numbers in there for the number of models your best guess will be required, and graph it out.

It doesn't sound that difficult... yet I must admit, I've not done the same for my personal goals over the next year... because it would be too large of a list.

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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/

Some links you may find useful as a relatively new contributor:

How Rosetta works, an explaination your cat will follow

Project Information Index

I see you are from Germany, here is a German translation of one of the QA threads. Perhaps you could help build a translation of the other QA thread to German.

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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/

I wish I could explain everything in a way that would be clear to everybody, but that is probably impossible in the amount of time I have. Instead, as suggested below, the discussion thread is a good way to get clear about what I am talking about--I check this, as do the many participants who know exactly what I am talking about and can explain as well as I can.

Milestones are a good idea, but most are pretty technical--I'll try to give a better idea of what our specific goals are with each of the projects as I discuss them in my journal. of course, the overall goals are very clear, for example to design an HIV vaccine that works! the problem in scientific research is that isn't always totally clear how to achieve the goals, and that is why we are trying many different approaches (our Gates foundation grant is supporting 6 different approaches to the vaccine design problem!). this makes rosetta@home a bit more complex than most other distributed computing projects which focus on a single large calculation or sets of calculations.

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I wonder if something we had at Find-a-Drug could help out in some of these issues. (learn from find-a-drug/thinks many years of experience at DC)
Though I don't know if the query groups and if there is anyone willing to help out implement it.
It worked very well over there for letting people know what they where doing, how far along that target we where and a little about it.

http://stats.find-a-drug.biz/oldquery1.html
along with the live target gives a list of all the target protein configuration attemptes, (live is where they where when they where being run :- and showed the % through the query type)

These all linked to the description page http://www.find-a-drug.org/hiv-frame.html telling you a litle about what and whay we where doing it.
Plain and simple and easy for all to see. Rather than burried down in lads of posts in the message boards.

It also creates a nice log of the information.


My idea is similar to that.
You put the query (task group or whatever you call it) in to your database as you load it, at the same time you could enter a description about what and why). You can then pull this information into a table and shows the percentage through that task. I assume you have a target number of itterations to do, though if you do need to alter it its just a number you alter and the percentage bar adjust accordingly.
You could even (if possible) mention the current lowest rmsd etc at the same time. I know it is not in the boinc framework, but it's just databases and table manipulation isn't it ;-)

I think that would
a) save you time posting in the forums about each target.
b) make it so much easier for us participants to know what happening. what we are doing without digging through all the current and previous posts.
c) ...

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Team mauisun.org

Hey! ...a step in the direction of showing milestones and project progress. You can graph your results as compared to the rest of the contributors.

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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/