DISQUS

I really think that the tools are not the bottleneck at this point. You're right we just need to do what needs to be done. We have to take the plunge without a guarantee of what the reward system will look like.

As for back-ups, Wikispaces gives you the option of dumping the whole site into a zip file either as HTML or Wikitext at the click of a button.

The choice of blog or wiki depends a lot of what your requirements are. The ability to track versions is critical for us since an experiment can take some time to completely report and interpret.

Just like in a paper notebook, a table of contents is a small price to pay for quickly accessing experiments and easily done in a wiki.

For a quick look at some screenshots of what I am talking about see slides from my talk in Manchester yesterday:
http://www.slideshare.net/jcbradley/manchester-...

We've also been using a wiki as lab notebook for 2.5 years and it has stood the test of time. Since our aim is to make our data public we make extensive use of GoogleDocs, Flickr, YouTube, etc. A blog linking back to individual lab notebook pages on the wiki makes it easy to discuss higher level concepts while providing links to the fine details should anyone care to probe further.

We've collected all these exhibits on my laboratory space on the South East corner of ACS island (in the skylab) for convenience. There are also some posters there from some of my students in my organic chemistry class.

That's awesome that you can make it!

It will be interesting to see how this evolves differently from Second Life - there are people busy connecting SL to real world devices. The benefit of Second Life right now is the magnitude of the networking opportunity, not so much the technology.

I think we're already seeing real collaboration in SL and people are doing things on there that can be done better there - like having meetings.

Here is an example of what Rajarshi is talking about:
http://usefulchem.wikispaces.com/D-EXP014

It would certainly be helpful for others to try to replicate his results using just the information on that page. That way we could learn how to report the docking runs better.

We also have a blank discussion section on that experiment. If we get any feedback - good or bad - that is where it would go.

Links to other docking runs:
http://usefulchem.wikispaces.com/combiugi

Thanks for posting!

I think you'll enjoy Wikispaces. Although the visual editor is pretty good for getting things done quickly, use the text editor to fix formatting issues. And the automatic CC license is very handy, especially if you don't know how to include the required HTML so that Google will identify your pages with the correct license.

Well different people will have different opinions about the "seriousness" or "value" or "validity" of our scientific information. What really counts is the opinion of people who want to make direct use of that information to do a reaction. And that is where the availability of the raw data comes in to convince the researcher.

It was good that we had a chance to discuss this issue a few times at the science blogging conference.

Ambarish,
This was exactly the discussion we had at a recent workshop at NIH:
http://usefulchem.blogspot.com/2008/01/crowdsou...

Yes, I think drug discovery and development can benefit from more openness.

I added a Deepak Singh to my network but not sure if it is the right one :)

Yes I think alternative funding models could be very helpful, even necessary for Science 2.0. One of the selling points for UsefulChem and Open Notebook Science in general is that the complete transparency should be of great value to funding organizations - they get to see in real time how their money gets spent. I've tried to make that case with foundations but no takers so far.
But this is going to mean getting real on all levels. As you say, proposals are written in a way to game the system often and it is hard to compete with that using transparency. A good example of that is the common practice of result hoarding - sending a "plan" that has a good chance of working because some of the work has been done but not yet published. In reality we can plan very little of true research because we can't anticipate "unexpected findings" by definition. And with ONS it is not possible to hoard. (That doesn't mean that we go into a project completely blind - just that we have to be realistic about how specifically we can forecast what we'll be doing in 3-5 years)

I think a system that involves the participation of the funding organization on a daily basis is much more realistic. And by design ONS permits that. As soon as we get assay results everyone knows about it and that is the time to discuss what they mean, not in the yearly progress report.

Of course IP control is out the door with ONS so any of the systems you mentioned based on that are not applicable. It would be more relevant to funding for orphan/3rd world diseases.

Nice summary. Indeed meeting you at SciFoo was a high point. The fun thing about working in the Science 2.0 area is that a lot can happen in a year and it makes it very unpredictable. I think a lot of smart people are lurking in the blogosphere with some strong ideas but haven't yet pulled the trigger.

One of the reasons I switched from neuroscience to chemistry as an undergrad is that I didn't like causing suffering to the rats. For some reason we switched from chloroform to CO2 as a method of killing. They convulse for several minutes before dying.

Yes, I agree that animal testing is necessary at some point in research. Luckily we now work at the level of in vitro testing so ethics is a non issue.

I've been looking for an adequate free way to search for audio within my podcasts but the reality is that the technology is simply not there. Yes, some simple words can be caught by services like PodScope but certainly not technical chemical terms.

What I ended up doing is just payed for the transcription using CastingWords, which worked out to a few hundred dollars a term. For example, my introductory organic chemistry classes (vodcast, podcast and Flash screencast) are available here:
http://chem241.blogspot.com/
and the transcript is here:
http://chem241transcripts.blogspot.com/

Since CastingWords has actual chemists on board, the transcript is pretty good, though not perfect.

By the way, although MIT OpenCourseWare has over 1700 courses listed, only a few dozen have complete video:
http://ocw.mit.edu/OcwWeb/web/courses/av/index.htm

From my personal experience with health problems I have found the stories from regular people on public discussion boards to be invaluable because they provide scenarios, which are lacking from clinical studies.

The problem is that by reducing everything to abstract correlations of averaged metrics you lose the multi-dimensional information of anecdotes.

Knowing that 70% of a population obtained some symptomatic relief with a certain drug does not help me predict if it will be useful for me specifically.

I had an arrhythmia problem for most of my life that no doctor was able to completely control. It is only when I went to discussion posts looking for people with the same types of symptoms and similar history to mine that I discovered the right medicine - and also the right dosage (which was key in my situation) that was finally effective.

Many people experiment for years trying to fix their health problems and their experience can be very useful.

Of course you take that information and consult with your doctor to make sure it is safe before trying anything.

Jing looks very interesting - what are the limitations compared to Camtasia?

Hey there's nothing wrong with furry creatures :)

I've been struggling with translating our UsefulChem knowledgebase into something more semantically marked up for machine (or human) use. One of the key challenges is that current approaches rely on "facts" rather than the reality that scientific information is always fuzzy. A big part of maturity in science is the ability to recognize how reliable a piece of information is from the context. New students are generally not great at doing this.

For example, we have reactions where the students reported a certain amount of compound was added. In a traditional paper, because you don't have access to the raw data you take this to be a fact. But when you are given NMRs of the reaction mixture you find that the measured ratio of compounds is not exactly what you would expect. So the experiment is compromised but it doesn't mean that a tremendous amount of useful information can't be derived. For example we can infer that all the products are stable (or not) in the solvent used for the reaction. But the concentration is "fuzzy" and we need to use fuzzy logic as scientists to process what the results mean.

That has also been a pet peeve of mine. What people now call nanotechnology - doing anything at the "nano" scale is not new for the most part. By that definition anything a chemist does is nanotech because they manipulate molecules.

The kind of thing Eric Drexler was talking about in Nanosystems is true nanotechnology - building complicated machines at the molecular level that actually do something useful.

As long as we reward people to hype they will continue doing it. This is one reason I think that trying to "quantify the quality" of scientific posts on social software using votes and citations is dangerous. The truest represention of a scientific experiment is usually the dullest. But that is a rant for another time....

That would be nice - I expect you'll be one of the first to report on it if or when it happens...

This could be useful for us if there are some open components. Do you think this will be all-pay closed service? I can't tell from the description.

I agree with you. Once the information genie is out of the bottle, you can't stuff it back in. The reason is simple - no matter how many people think information should not be free it only takes one person in the world to publish it. And with plenty of options for free hosting and indexing there is no cost barrier to that.

Just take what has happened to open course content. Many teachers wwere (and still are) paranoid about keeping their online class content closed. But it only takes one teacher in the world in a particular discipline to blow that up. A year after I started posting my recorded lectures in organic chemistry online, several other professors did the same thing, further enriching the global learning base. The same thing with textbooks - there are now several high quality university level organic chemistry textbooks freely available online. But most publishers still think that copyright control is the only card they can play.

Nice review! You are right - it is really unclear how all this will be used and I don't have any burning desire to upload my personal health info anytime soon.

It did sound a little sininster that your Firefox was acting strange afterwards :)