Wednesday, February 25, 2009

ONS Solubility Challenge on Sigma-Aldrich tech sheet

The Open Notebook Science Solubility Challenge has made it onto the Solubility Information for Products technical sheet of Sigma-Aldrich:
Sigma-Aldrich are currently collaborating with Nature and Submeta in an Open Notebook Science Challenge. This is a project aimed at facilitating the generation of solubility information for chemicals. Please follow this link 'Open Notebook Science Challenge - Solubility' for more information on this project.
This is a great example of how synergies between academia, industry, publishers and foundations can take place quickly and in the open.

There is some other interesting information on that page - notably a table translating written descriptions of solubility terminology - like "freely soluble" - into numbers.

Labels: , , , ,

Tuesday, February 24, 2009

Open Notebook Science Claims and Logos

I have recently posted about definitions relating to Open Notebook Science. When I discuss ONS without qualification I generally refer to providing access to the entire lab notebook and associated supporting raw data in near real-time. As I explained in that post, only when these two criteria are met do you get the full benefit that anyone (human or not) can see what you have and have not done and can realistically contribute the next step in a project without having to contact the researcher (human or not) for more information.

I have also conceded that this is not necessarily an option for everyone interested in performing research more openly. Others (Dave Bacon for example) have suggested that more restrictive forms of ONS could be useful, especially when intellectual property protection is involved. Dave called this Pseudo-ONS and I have suggested Partial-ONS: both abbreviate to PONS.

This has been a tricky distinction to make quickly and the idea of logos for ONS has been kicked around. When Hope Leman asked me for an ONS logo I thought I would ask Andy Lang to create something and deal with this issue at the same time.

Inspired by the Creative Commons system, we set up an ONS claims page to link from the logos to descriptions. The options are AC (All Content) vs SC (Selected Content) and I (Immediate) vs D (Delayed).

Let us know what you think.


Wednesday, February 18, 2009

ONS talks at the British Library, ACRL and a Slideshare feature

Update: the Columbia panel on Open Science video is now available.

This past week I gave two talks and participated in one panel discussion - with no jetlag or airport burn-out. Gotta love technology for allowing for that to happen.

My first talk was on Feb 11, 2009 at a session on Digital Lives at the British Library. This was a hybrid conference with a presence in the physical world as well as Second Life. I could see and hear the speakers in London from within Second Life and I'm assuming they saw my presentation just as clearly. Joanna Scott from Nature coordinated the SL session.

I then participated in a panel in Second Life on "Stepping into Science" on Feb 13, 2009. There was as good discussion about using Second Life for educational applications. The other panelists included:
  • - Troy McConaghy (Scientist and Educator who has been involved with Second Life for over three years)
  • - Dr. George Djorgovski (Caltech and Meta Institute for Computational Astrophysics (MICA))
  • - Joanna Scott (Writer for Nature and manages Second Nature on Second Life)
  • - Adrienne J. Gauthier, M.Ed. (Instructional Technology Specialist, Steward Observatory)
  • - Tony Crider (Elon University)
Then on Feb 17, 2009 I presented for the Association of College and Research Libraries using Acrobat Connect Pro. Hope Kandel from LearningTimes did a great job in coordinating the technology and people several weeks before the event. The attendees used chat to ask questions during my talk then John Howard moderated by summarizing some of the questions verbally at the end. It went well I think.

And I just heard that my ACRL presentation on Open Notebook Science is currently showcased on Slideshare under the Education category.

Now I'm on my way to a physical conference at Columbia with Bora: Open Science: Good For Research, Good For Researchers?

Labels: , , ,

Monday, February 16, 2009

Prize for Spectra Game

Tony Williams and Andy Lang have been busy over the weekend adding a pile more spectra to the Spectra Game on the web. I used it this morning in my workshop for CHEM242 and I think it is time to announce a prize.

During the month of February 2009, the first student in the US (undergraduate or high school) to score 100 on the H NMR web version of the Spectra Game will win a molecular model kit. Obviously all of my students taking organic chemistry CHEM242 are eligible but I invite the rest of the country to give them some healthy competition.

Make sure to add your email when you start playing the game so that we can contact you if you win.

Play the Spectra Game


Saturday, February 14, 2009

Web based Spectra Game

Yesterday I used the NMR game in Second Life during our 2-hour Friday workshop in CHEM242. (We used a new location on Drexel island SLURL) The students who attended had looked at little or no material prior to the workshop. By the end I ended up explaining chemical shifts, complex coupling patterns and diastereotopic hydrogens differentiated by the presence of a chiral center. The only concept we didn't cover is integration, although we used peak size to take a guess about groups with lots of hydrogens (like trimethyl).

I think it was a very efficient way to teach NMR and the students can now go off and continue to practice till our next workshop Monday. Second Life has some advantages - such as the ability to mediate group study sessions where students from remote location can come together to play and discuss spectral assignments using either voice or chat. It is also nice to see the molecules in 3D, especially for bridged cyclic systems.

However, there is a bit of a learning curve to get into Second Life and not all computers have a suitable video card. So it is nice to now have the ability to play the game on a web browser. Andy set up the game play so that the score reflects the number of correct answers obtained in a row. There are also only 3 molecules to choose from instead of 5 in Second Life.

We're using JSpecView to render the spectra so expanding peaks simply requires dragging the mouse across the area of interest. It is also possible to integrate and view the metadata by right clicking.

Currently we mainly have H NMR spectra but we'll be adding lots more C NMR, IR, UV, MS, etc. It all depends on how many Open Data contributions we can find. If anyone has spectra to donate please upload them to ChemSpider and don't forget to check the box for Open Data.

This has been a wonderful example of rapid collaboration by Andrew Lang, Rajarshi Guha, Antony Williams, Robert Lancashire and myself.

Give the web Spectra Game a spin and see if you can beat the high score....

Labels: , , , , ,

Thursday, February 12, 2009

Substructure searching on ONS solubility data

Jenny recently reported that one of her values seemed low and was going to repeat it. She obtained 0.9 M for 4-hydroxybenzaldehyde in THF (ONSC-EXP057). Compared against the previous value of 3.5M (UC-EXP208) it certainly seems like one of the values is off.

To get a better idea of which it might be it can be useful to look at the solubility of structurally similar compounds. We can now do this using Rajarshi's web query tool by entering information in the SMARTS box. In this case we want to do a substructure search based on the skeleton of 4-hydroxybenzaldehyde. Putting the SMILES of that compound (O=Cc1ccc(O)cc1) in the SMARTS box and selecting THF returns 6 results.

It certainly does seem that 0.9M is low for that group. More measurements will settle the issue.

Labels: , ,

Open Notebook Science, Reproducibility and Exclusion

There has been a fairly active conversation about Open Notebook Science over the past few days on FriendFeed. Some of the points I have wanted to make wont fit there so I'll post them here.

A short definition of ONS on Wikipedia: Open Notebook Science is the practice of making the entire primary record of a research project publicly available online as it is recorded.

I have repeatedly said that Open Notebook Science is probably not the best choice - at least initially - for most researchers interested in dipping their toes into Open Science. So why do I care so much about pursuing it?

It has to do with taking us past the tipping point to runaway real time open collaborative crowdsourcing in science.

There are two properties of ONS that at least set the stage for such a scenario.

1) Reproducibility: The primary purpose of a laboratory notebook is to make experiments reproducible for the researcher who recorded it. You can't improve on a process if don't keep a detailed record of what exactly happened in a given trial. A secondary purpose is to prove what a researcher knew and did at a specific point in time. This can be useful for patent enforcement if the notebook is kept private. There are other applications, but in general the sharing of experimental details is typically extremely limited in science.

I believe that this is an artificial barrier still standing to a large extent because of inertia. In the past, even if they wanted to, researchers could not realistically make this information public because of the absence of a convenient publication vehicle. But that is changing right now - technology is no longer the bottleneck. Very high quality free hosted services exist now that permit sharing with very little additional effort. All we have to do is record our laboratory notebook (which has to be kept anyway) on media that are easy to share and automatically indexed on major search engines.

By definition, the notebook should have all the information necessary to reproduce the results you obtained. If it is published in close to real time, someone who doesn't know you can read the details of an experiment you did today and contribute to the advancement of your project tomorrow. Or they may use your information for their own project. As long as they also maintain an Open Notebook knowledge can spread extremely rapidly. The efficiency of such a system between strangers is probably far greater than most scientific collaborations between researchers who already know each other.

2) Exclusion. If I come across an experiment you did yesterday and I have a desire to contribute meaningfully to your project, before executing the next experiment, I will want to look at all of the related experiments in your notebook. Of particular interest will be "failed experiments" to avoid repeating the same attempts. Or I may want to repeat one of your failed runs because I don't think that you properly controlled some parameter or made a mistake in the analysis.

The point of an Open Notebook is to get the truth - the whole truth about what you did and did not do. If I don't find what I am looking for in your notebook - and you have declared it to be an Open Notebook - then I can safely assume that you have not done it and I will feel confident to invest my resources to do that next experiment.

For an example of this system at work consider the Open Notebook Science solubility challenge. If I want to contribute to the project, the first thing to do is take a look at what has not been extensively measured yet. I can do this via the web query or directly on the experiment list page. By using the web query tool I can also look for contradictory results and try to resolve them. Or I may wish to include a control in my measurements and pick a compound that has been measured reproducibly using different techniques. I probably also want to look at the minute details of exactly how previous researchers applied their technique.

Now what would happen if we had adopted a Partial Open Notebook Science approach where we delayed recording lab notebook pages until a paper was published? Or what if we used the PONS variant of only recording experiments that "worked"?

Had we done anything short of a fully Open Notebook the project would have never gotten off the ground.

Labels: , , ,

Saturday, February 07, 2009

NMR game on Second Life

Andrew Lang and I have been discussing publishing our work on chemistry and Second Life. We're working on the draft here. When going over the game section, it became clear that we'll probably need to make two manuscripts out of this. This is an opportunity to wrap up my previous work on the EduFrag project - using Unreal Tournament to teach organic chemistry. I had submitted that article but as it was going through the peer-review process the approach was essentially made obsolete when we adapted the quizzes to Second Life.

So Andy and I brainstormed some new chemistry games that we could introduce to Second Life to leverage our recent tools. One of the applications is the NMR game. By combining the orac molecule rezzer, the SL spectral viewing tool and ChemSpider Open Data spectra I think we have a pretty good game.

The idea simple: click on the molecule that is represented by the spectrum. If it is correct you get 2 points and get another spectrum. You lose a point by clicking on an incorrect molecule. After going through all the spectra your score gets posted on the web to a top10 list. For equal scores the best time takes it.

From an educational perspective this is useful I think on several levels.

First the ability to look at the molecule in 3D makes it easier in many cases to demonstrate the relationship between Hs, which is critical in NMR.

Second we are using real spectra - not simulations. That is a great opportunity to teach students about how to deal with impurities, solvent peaks or quirks in the peaks. The viewer allows for easy zooming by typing commands like "zoom 1.5-2.5" in the chat box.

Third this spectrum viewer uses Open Source JCAMP-DX files so it can (and will) be adapted to all kinds of spectra - like IR, UV, MS, C NMR, etc. I'm teaching (CHEM 242) all of those techniques this term so I'll have an opportunity to see how well it works.

There is currently a copy of the game on ACS island (SLURL) - give it a try and give us some feedback.

Here is picture of the game area (Viv is sitting on the molecule and I'm on the spectrum):

Friday, February 06, 2009

C&E News article on ONS and FriendFeed

Carmen Drahl's article following her visit to my lab has just appeared online on Chemical and Engineering News:
(February 9, 2009 Volume 87, Number 06 p. 34).

I think she really captured the essence of our Open Notebook Science solubility project and how to make those results available in an intuitive way via web queries and Second Life tools. Rajarshi Guha and Andrew Lang's work is demonstrated here. The text description is very helpful but it is her video recordings that really stand out. There are two screencasts from Second Life: one from my class where I ran an organic chemistry quiz race and another demonstrating the Ugi solubility explorer.

Carmen also recorded a very good overview of how we use FriendFeed to collaborate with other researchers. The life science and Open Science communities are very strong right now on FriendFeed and hopefully this demonstration will encourage more chemists to participate. To illustrate how easy it is to connect with new people she shows how the "like button" enabled a link to be formed when Egon Willighagen liked one of her posts.

Labels: , , , ,

Tuesday, February 03, 2009

Sigma-Aldrich ships ONS solubility challenge batch

A while back I reported that Sigma-Aldrich was sponsoring the Open Notebook Science challenge by donating compounds when necessary. That was a very generous offer and we have just made use of it. The first batch has shipped yesterday to Jenny Hale at Southampton University. Since she is using a SpeedVac to measure solubility, we made a list of lower cost Ugi product reactants with higher boiling points. Here is the collection:

Every solubility measurement technique has its pros and cons. Evaporation based methods are very direct but are limited to high boiling solutes. UV is sensitive to low concentrations but requires a calibration curve and a chromophore. (for example EXP024)

NMR is less sensitive than UV but has the advantage that it can handle solutes of any volatility and does not require a chromophore - and from an efficiency standpoint - it does not require a calibration curve. At our concentration range of interest (>0.1M), NMR does seem to be the most convenient method in my lab: make a saturated solution in the solvent of interest then dilute with a deuterated solvent (generally CDCl3) then add an internal standard (acetonitrile is handy) then take one spectrum and analyse. For an example see Khalid's EXP030.

For an sampling of all the methods see our experiment list.

Labels: , , ,

Monday, February 02, 2009

David Bulger is Feb09 Submeta ONS Award Winner

David Bulger, a chemistry undergraduate student working under the supervision of Robert Stewart at Oral Roberts University, is the February 2009 Submeta Open Notebook Science Challenge Award winner.

In addition to a cash prize from Submeta, he will receive a one-year subscription to Nature magazine. David is focusing on NMR techniques to measure solubility. See his experiments here:

Seven more Submeta ONS Awards will be made during 2009. Submissions from students in the US and the UK are still welcome.
For more information see:

Labels: , , ,

Sunday, February 01, 2009

Maintaining Solubility Data Provenance from Wikipedia to Lab Notebook

I recently noticed a bunch of incoming clicks from the Wikipedia entry for benzoic acid to our Open Notebook Science solubility challenge wiki on the ONSC sitemeter.

It turns out that Andrew Lang added a link from the Properties section covering the solubility of benzoic acid in a few organic solvents.

Instead of pointing directly to the individual notebook pages for each measurement, clicking on the reference takes us to a page summarizing all of the solubility measurements of benzoic acid in various solvents. The values are averaged and a standard deviation is provided.

Clicking on one of these links takes us to a summary page of each measurement for one of the solvents.
Clicking a link from that collection takes us to the laboratory notebook page (for example EXP005) on the wiki and ultimately to a Google Spreadsheet (for example) with all of the calculations for that measurement.

The beautiful thing is that the original url can't be any easier to create: acid

And this same link will always link to the best possible values as more measurements are made and erroneous values are removed if found. With Andy's current code, if measurements at different temperatures are made, a plot is provided.

Now we're getting into some interesting territory. It is now so simple to refer to the solubility data of the ONS challenge that people who don't know the first thing about wikis, blogs or coding can start to partcipate in the use of ONS measurements.

The Open Notebook can be thought of like insurance. We don't want to have to use it - but if there is a problem we have to ability to trace the chain of provenance all the way to the source.

By the way notice that this is the only link in the Properties section of this Wikipedia article with a reference...

Labels: , ,

Creative Commons Attribution Share-Alike 2.5 License