Marshall Moritz is July09 Submeta ONS Award Winner

2009-07-01T10:46:23.838-04:00

Marshall Moritz, a chemistry and math student at Syracuse University, working under the supervision of Jean-Claude Bradley at Drexel University over the summer, is the July 2009 Submeta Open Notebook Science Challenge Award winner. He wins a cash prize from Submeta.

Marshall started out using NMR to measure solubility and recently has made some important contributions to the Challenge by using the sequential precipitation technique to obtain solubilities in different solvent mixtures at various temperatures. See his experiments here:
http://onschallenge.wikispaces.com/list+of+experiments

Three 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:
http://onschallenge.wikispaces.com
http://onschallenge.wikispaces.com/submetaawards08

Handling reactives in the solubility database

2009-06-29T09:17:50.887-04:00

The discovery that aromatic aldehydes bearing electron withdrawing groups react with alcohols has forced us to create a new category in the ONS Challenge SolubilitySum spreadsheet: solute reacts with solvent. There is now a column on the far right to flag these.

Since there is no meaningful number for these mixtures we are assigning the value of -0.1M in the solubility column of the SolSum sheet. That has the advantage that it will not break any web services currently querying the sheet. We can also put an explanation in the notes column for a reason, such as "forms hemiacetal".

One of the benefits of this approach is that all solutes reacting with solvents can be queried using Rajarshi's web query setting the solubility range from -1 to -0.01 M.

Solubility surfaces in 3D

2009-06-26T13:22:27.176-04:00

After a little bump in the road with attempting to measure the solubility of 4-nitrobenzaldehyde in methanol, Marshall Moritz extended the study (ONSC-EXP111) to chloroform and acetonitrile, where no hemiacetal can form. The sequential precipitation method seems to work quite well with a new thermostated bath that lets us go down to almost -30C.

The values in pure acetonitrile and chloroform were consistent with those obtained from Maccarone, E.; Perrini G. Gazetta Chimica Italiana. 1982, 112, p. 447. (private access). But Marshall went further and measured 9 points with mixed solvents and different concentrations. The result is this saddle shaped 3D surface plot.


I think the potential for extending the ONS Challenge to cover the full multi-dimensional space of mixtures of about 10 common solvents and temperature is very exciting. It would be foolish to think that we can map in extreme detail such large surfaces. However, I'll bet we can come up with some useful estimates of what the surface looks like in many areas of the space.

The long rage plan for this approach would involve coming up with at least an empirical model based on molecular descriptors of the solvents and solutes. This would help predict the space for completely new combinations.

Being able to predict the solubility of all starting materials and products would enable organic chemists to rationally select solvent systems and temperatures for their reactions maximizing product yield from simple precipitation. This is something that we are investigating for the Ugi reaction and I'll report on this as the data come in.

NMR integration progress for solubility measurements

2009-06-25T09:58:14.002-04:00

In a previous post I reported about issues with using H NMR integrations for quantitative assessment of solute concentration to determine solubility. Using default parameters, a study by David Bulger revealed that integration of the methyl group on 2-phenylbutanoic acid lead to only 8.4% average error while the methine H gave an average of 26% under-integration.(ONSC-EXP102)

We have tried to select methyl or methylene groups whenever possible but obviously this won't work for many compounds, especially our series of aromatic aldehydes and carboxylic acids.

Khalid Mirza has just done a study using longer relaxation times and the results appear very promising (ONSC-EXP103). For 4-pyrenebutanoic acid using default parameters the integration of the aromatic vs. methylene hydrogens was off by 9-18% while extending the relaxation time (d1=50s) reduced the error to less than 1.2%.

Furthermore, Marshall Moritz used the new settings in a measurement of a known concentration of 4-nitrobenzaldehyde in acetonitrile and came within 3.2% using an aromatic hydrogen (ONSC-EXP111). Use of the aldehyde hydrogen was not as good, although much better than what we normally see with the default settings.

So I am cautiously optimistic that we are likely to get better data going forward.

Complications with solubility measurements of aldehydes in alcohols

2009-06-22T18:24:18.933-04:00

Last week I mentioned that we had started measuring temperature solubility curves. Since 4-nitrobenzaldehyde in methanol also got flagged by our Outlier Bot we picked it as the next one to process. This one has bothered me for some time because our values have systematically come out to about half of those published by Maccarone, E.; Perrini G. Gazetta Chimica Italiana. 1982, 112, p. 447. (private access) In this paper temperature curves for the solubilities were also provided and so I thought this would be a great opportunity to validate our sequential precipitation method.This experiment (ONSC-EXP110) turned out to be very puzzling. On the day that we tried to make solutions we could not get as much material to go in as expected from the paper, even by sonicating at 40C. The next day some of these samples went into solution and then we could not get precipitation to occur for some samples even at 0C.However, an examination of the NMRs of the samples with lowest concentration revealed the problem. It turns out that they were about 50% converted to the methanol hemiacetal. The NMR clearly shows the coupling between the benzylic and hydroxyl protons at 5.6 and 6.8 ppm, each integrating for 1H each compared with 2H for each of the new peaks in the aromatic region.It turns out that the hemiacetal was present in all our previous measurements for 4-nitrobenzaldehyde in methanol but we didn't spot it. Furthermore we found significant hemiacetal formation for 2-chloro-5-nitrobenzaldehyde, 2,6-dichlorobenzadehyde and 4-chlorobenzaldehyde but only trace on none for others like veratraldehyde (ONSC-EXP033 has several of these NMRs). So it appears that if the aromatic ring bears sufficiently electron withdrawing groups hemiacetal formation is facilitated without the presence of a catalyst. This makes sense from a mechanistic standpoint.Since the hemiacetal forms so easily in these cases I wonder why there was no mention made of it in the Maccarone paper. They assayed concentration using GLC - perhaps the hemiacetal decomposed quickly under those conditions? (PNBA is para-nitrobenzadlehyde):From a practical standpoint is it even possible to measure the solubility of 4-nitrobenzaldehyde in alcohols? If you try to make up a solution for a reaction the concentration will be much less than calculated. With an excess of alcoholic solvent it seems unlikely that a reaction consuming the aldehyde will shift the equilibrium enough to make the formation of the hemiacetal inconsequential.I think that for the Ugi reaction the implication of this is that alcoholic solvents should not be used for aldehydes bearing electron withdrawing groups.[...]

On the Advisory Board of Chemical and Engineering News

2009-06-18T05:18:09.066-04:00

I have accepted an invitation to join the Advisory Board of Chemical and Engineering News. The three year appointment involves yearly meetings in Washington, D.C. where important trends in chemistry and the focus of the magazine are discussed.

Many thanks to Carmen Drahl for putting my name forward!

BrightTALK on ONS and Drug Discovery

2009-06-16T09:50:22.516-04:00

I will be presenting at the BrightTALK seminar series on July 23, 2009 at noon ET. The virtual presentation will be on "Open Notebook Science for Collaborative Drug Discovery".

Temperature solubility curves using sequential precipitation

2009-06-16T06:37:01.676-04:00

We were going to wait for a while to tackle temperature related solubility because it wasn't clear that our NMR technique was applicable. The main problem is that separating out the supernatant at a given temperature can be tricky for both filtration and centrifugation with our available equipment.

However, while discussing the issue with Marshall last week it occurred to me that we might be able to get the data by sequential crystallization. The idea is to prepare several solutions at known concentrations at a high temperature then let the bath cool down and note the temperature when precipitates are first observed. We can then intrapolate to report the solubility at room temperature if necessary.

Khalid and I made an attempt on Friday for pyrene in acetonitrile (EXP109) and obtained a value of 0.16 M at 22C, about twice the value found by Marshall in EXP108 using NMR. Part of the discrepancy is probably related to longer relaxation times of aromatic protons but we have to keep in mind that NMR is not particularly precise at such low concentrations. Hopefully we will soon figure out how to run our NMR experiments to allow full relaxation of all protons and address this issue more conclusively.

Crowdsourcing solubility requests from bots and people

2009-06-14T14:37:29.674-04:00

Now that we have a reasonably routine way of measuring non-aqueous solubility and students trained to do the measurements, we can think about adding some structure to the workflow. By using an open Google Spreadsheet to list the next solute and solvent to measure we can easily crowdsource the requests. This is the dosol sheet and students are instructed to check it before planning their experiments for the day.Requested experiments come from the following sources:1) OUTLIER BOT: Andrew Lang has created a neat service that reports measurements exceeding a provided standard deviation to mean ratio (plug into the URL) and a Grubbs outlier threshold. Currently, the "bot" does not automatically write to the dosol sheet but eventually I see that it would make sense to complete that integration. On a daily basis I run it and process the flagged entries in the following ways:a) If I investigate the corresponding lab notebook pages and find an error in the calculations I simply fix it.b) If I find that one or more of the measurements are obviously in error I mark the entries as DONOTUSE in the SolSum sheet. This is often a low value that was obtained early on in the project before we appreciated how much mixing is required for some solutes.c) If I cannot determine why there is a discrepancy I place a request on the dosol sheet. (note: solubilities that are very low ([...]

Recent insights about solubility measurements

2009-06-12T09:25:59.133-04:00

Over the past several months we have learned a lot more about measuring non-aqueous solubilities. (see experiment list) Here is a summary:1) Sonication: It can be really difficult to reach saturation for some compounds. Since we started the ONS Challenge project in the fall of last year students have used all kinds of methods to mix the solvent and solute. For a while we required that solid remain during 10 minutes of vortexing. However, this proved problematic for doing lots of samples in parallel and required the researcher to stand there holding the vials on the vortexer.So to be able to leave samples mixing unattended we started using a sonicator. This certainly seems to be a major improvement over vortexing. But, as an unintended benefit, sonication also caused the temperature to rise. Upon cooling to room temperature, additional solid is often observed to come out of solution - the only sure guarantee that saturation has been reached. Our current protocol is to continue to add solute until 30 minutes of sonication leaves solid in the vials. Temperature of the bath is also taken before and after to ensure reproducibility.2) Screw Cap Vials: One of the problems with sonication and increasing temperature is that standard one dram vials with caps that snap in often pop out. Using half-dram vials with screw caps completely solved that problem.3) Filtration, centrifugation and decantation: Coming up with a common protocol to separate the supernatant after saturation is reached is not as straightforward as it might seem. The problem is that saturated solutions can behave quite differently. The easiest behavior to deal with is when the solute just settles on the bottom and simple decantation can be used. This typically happens for low solubility cases where the solute is much more dense than the solvent. In other situations a suspension forms that does not settle quickly. Centrifugation for a few minutes often resolves that issue and then the supernatant can be decanted. However, there are more difficult suspensions that do not settled after centrifugation. The worst of these actually form a gel. We have found that filtering through as Pasteur pipette packed with a small piece of cotton usually does the trick. The gel or suspension is transferred into the pipette and a bulb is carefully squeezed to try to get at least a drop of supernatant out. Even getting a single drop can be challenging sometimes so it is fortunate that our NMR method does not require accurate volume measurements.4) Evaporation of supernatant: Sometimes we observe higher solubilities than the known saturation values. This was puzzling because looking at the NMRs it was clear that the ratios of the solute to solvent were real. We traced back this problem to the way the supernatant is handled. When the drop is introduced at the top of the NMR tube it rolls down and a significant amount of solvent can evaporate. When the deuterated solvent is then added the ratio of solute to solvent will appear to be much higher than it was in the saturated solution. This is especially problematic for volatile solvents like THF. A similar effect can be caused by waiting too long to take the NMR as solvent does evaporate slowly even with a cap on. The solution to this problem is to transfer the drop of saturated solution directily into a vial containing the deuterated solvent and taking the NMR immediately.5) Deuterated solvent considerations: We have also had problems with solutes precipitating out when diluted into the deuterated solvent. Polyphenols in DMSO or THF tend to do this when diluted in CDCl3. In this case diluting in DMSO-d6 resolves the issue. If a solvent other than DMSO is used non-deuterated DMSO can be added to DMSO-d6 to conserve deuterated solvent. Its only purpose is to enable l[...]

David Bulger's Drexel visit

2009-06-09T18:56:19.232-04:00

David Bulger (February 2009 Submeta ONS Challenge winner) from Oral Roberts University just completed a two week visit in my lab at Drexel - thanks to the generous efforts of Andrew Lang. It was truly a pleasure to finally meet him in person and for the students in my group exchange tips and techniques for working in the lab.

David got a lot done in that short time. On his first day he repeated a Ugi reaction (EXP223) known to work well so that he could learn how to do it and carry that knowledge back to ORU. He attempted several other Ugi reactions (EXP226 and EXP229) to add to our knowledge of conditions leading to precipitates. One of the experiments (EXP230) involved using a 96 well plate for rapid screening. Unfortunately, it was difficult to properly seal the wells and solvent evaporation was too problematic. We are always looking for methods to accelerate the execution of experiments so it was certainly worth trying and we learned something from the trial.

David also did several solubility experiments and resolved conclusively previously contradictory solubility measurements for 1-pyrenebutanoic acid (EXP091). Finally, he looked at the accuracy of our NMR technique for measuring solubility using known concentrations of 2-phenylbutanoic acid (EXP102). I'll be posting about this in more detail shortly as part of a post on what we have learned recently about measuring solubility. For more of David's solubility experiments see our experiment list.

David is now in the UK in Cameron Neylon's lab. His current experiments are reported here.

Matthew Federici is June09 Submeta ONS Award Winner

2009-06-01T18:23:18.053-04:00

Matthew Federici, a mechanical engineering student working under the supervision of Jean-Claude Bradley at Drexel University, is the June 2009 Submeta Open Notebook Science Challenge Award winner. He wins a cash prize from Submeta.

Matt has applied an NMR technique to measure solubility. See his experiments here:
http://onschallenge.wikispaces.com/list+of+experiments

Four 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:
http://onschallenge.wikispaces.com
http://onschallenge.wikispaces.com/submetaawards08

ONS talk at AI conference in July 2009

2009-05-25T10:08:56.474-04:00

I've been invited to talk at the IJCAI'09 Workshop on Abductive & Inductive Knowledge Development in Pasadena on July 12, 2009. This will be a great opportunity to focus what might become possible on the machine side of Open Notebook Science.

Although Ross King (of Robot Scientist fame) won't be there in person, his collaborator Oliver Ray will be giving a talk on their project. That should be quite interesting.

My abstract:

The Role of Openness in Scientific Automation: a case for Open Notebook Science

The use of Open Notebook Science to collect and make publicly available non-aqueous solubility measurements and the synthesis of anti-malarial agents will be described. ONS involves the real time sharing of all experiments and associated raw data by a community of collaborators who are geographically distributed and may have never communicated using channels other than these shared projects. Monthly cash prizes are awarded to participating students by means of the ONS Challenge Submeta Awards for solubility measurements. The laboratory notebook pages are recorded on a public wiki and the solubility measurements, including relevant calculations, are stored in public Google Spreadsheets. A combination of ChemSpider, the GoogleDoc visualization API and web services is used to enable flexible searching and display of desired subsets of the data.

The use of such a distributed and open platform with virtually zero read/write costs for the communication of science creates new opportunities for rapid collaboration. By using a redundant information dissemination system, channels that are more human friendly can be integrated with those that are more geared to machine readability. For example a publicly editable Google Spreadsheet tied to the operation of a robotic liquid handling system opens up the possibility of integrating crowdsourced intelligence with human workflows. In another example, web services called from within a publicly editable Google Spreadsheet to perform calculations on NMR spectra can be integrated readily with manually executed steps to accelerate progress and minimize the possibility of errors.

The advantages and disadvantages of ONS and related bottom-up Open Science strategies will be discussed. The key concerns revolve around intellectual property, trust, reference-ability, publication in traditional academic vehicles and other implications for collaborations.

Two new ONS Challenge Judges: Andrew Lang and Troy Milliken

2009-05-14T19:24:55.840-04:00

Bill Hooker and I have been contacting the chemistry departments in the US to recruit new students to the Open Notebook Science Challenge. As a result, I have the pleasure of reporting that today we have a new judge: Troy Milliken from Jackson State University. Troy is a polymer chemist and will look out for some promising students to supervise to contribute to our solubility measurements.

Andrew Lang from Oral Roberts University also agreed to participate as a judge this month. As a mathematician and creator of many of our web services to calculate and display solubility measurements, Andy is in a unique position to provide valuable feedback to our students.

This brings our total judge count to 7.

Baseline correction for automated integration of NMR JCAMP-DX files

2009-05-14T18:30:32.636-04:00

We were initially getting a surprisingly large solubility measurement for one of our solutes (spectrum from ONSC-EXP077). After investigating, it was clear that the discrepancy was originating from a peak with a sloping baseline:


The web service was integrating all of the area beneath the peak and the raised baseline. After discussing the situation with Andrew Lang, he modified his code to exclude the area beneath a linearly sloping baseline. Andy's code is Open Source and made available here, including detailed instructions for anyone wishing to implement it themselves. This modified web service is included in the most recent Google Spreadsheet template for semi-automated measurement of solubility using NMR.

The progress of science is a clumsy walk toward a non-attainable ideal of full understanding and control. With every experiment we have to re-question what think we know as variables change. This is why I am so passionate about Open Notebook Science and having all stakeholders interact at the level of the individual experiment. We caught this issue early and we were able to deal with it because our computational collaborator was engaged in details with the chemists and responsive.

Leaders and Pushers in Open Science projects

2009-05-09T09:44:34.321-04:00

Fred Zimny just posted an interesting piece on open scientific collaborations: Your (r)evolution will be digitized: online tools for radical collaboration — DMMThe article tries to give a balanced view of radical sharing and our Open Notebook Science projects (ONSchallenge and UsefulChem) get a mention.Some good discussions about what it takes to have an open collaboration succeed have emerged from it. Deepak Singh has posted about the requirement for a benevolent dictator. There is also a healthy discussion on FriendFeed where Andrew Lang argues for an organizer.I think that open projects function very much like any other projects, with the advantage of it being easier for people to join in and make use of the results. People often mention leadership as the key ingredient to making projects work. Leadership is associated with that nebulous concept of vision, a type of flexible long range planning that probably does work best when coming from a single individual.Leaders with a clear vision are known for giving inspiring speeches and presentations. But vision by itself does not get things done. For that you need pushers - people who relentlessly push themselves and others to execute. In the book "The Dip", Seth Godin explores the value of strategic perseverance and quitting. In anything worth doing there is a period after initial enthusiasm and before one can see the light at the end of the tunnel where most people quit - this is the dip. Godin argues that the key to being successful is to being able to tell the difference between a true dip and a pit leading nowhere. Winners strategically quit the dead ends and persevere through the dips. That is exactly what pushers do.People often think that successful leaders attract followers - people who are subservient. In my experience successful projects result from a collaboration of colleagues who share common values. Within the group there may be individuals with less experience who can best contribute by trusting those with more experience and making a firm commitment to learn quickly so that they can initiate contributions that count.Of course leaders have to be pushers themselves. But since people have a limited ability to maintain simultaneous goals with equal urgency, it is helpful for collaborating colleagues to act as pushers in a complementary fashion.To give a few concrete example of this, consider our Open Notebook Science projects.Andrew Lang has been a close collaborator for a long time and has written code that enables us to visualize our solubility results (with Rajarshi Guha) and process NMR files automatically. The project would be missing key components without Andy pushing to make things happen. But Andy has also initiated other high impact actions that are unrelated to writing code: our ONS Wikipedia entry, recruiting David Bulger at ORU to do solubility measurements and adding our measurements to common chemicals in Wikipedia - which has ended being a popular portal to our data. Bill Hooker, in addition to writing in depth about Open Science, has recently stepped up to help with emailing all of the chemistry departments in the US to get some more students to participate in the ONS Challenge. Shirley Wu volunteered to assist Andy in making ONS logos. Brent Friesen included the solubility challenge as part of his sophomore organic chemistry lab at Dominican University.Cameron Neylon has done a tremendous amount - recently he pushed to get a group of us to publish a chapter in the upcoming O'Reilly Media book Beautiful Data. Organizing my trip to the UK last fall was another major accomplishment that he made happen. Cameron speaks extens[...]

Streamlining automated solubility measurements with NMR JCAMP-DX files

2009-05-04T05:55:54.092-04:00

Two months ago I reported on a protocol for measuring solubility using NMR JCAMP-DX files and a web service set up by Andrew Lang called from within a Google Spreadsheet. Things were going well until David at ORU was a little too productive and crashed the server from too many requests.

Andy had to change the way the script worked and used this as an opportunity to make the service more broadly usable. It turns out that the compressed JCAMP-DX files produced by different NMR instruments are not created with exactly the same standards. A way to address that issue is to convert the files to an uncompressed XY format. Unfortunately, there was a glitch in JSpecView which created XY formatted spectra displaying in Hz instead of the standard ppm.

Now all of these issues have been resolved and the process is simpler than ever. Robert Lancashire fixed the glitch in the April 26, 2009 release of JSpecView. And Andy not only made his integration web service work for the new release but also created another service to display JCAMP-DX spectra directly from the the DX file (see here for an example). In the past students had to create an associated HTML file to display JCAMP-DX files and this was just another point in the process to introduce errors and slow things down.

The new process for the semi-automated measurement of solubility (SAMS) using NMR is as follows:

1) Make a saturated solution in a given solvent (sonicate for at least 30 mins - more on this in a separate post)
2) Transfer about 0.1 mL to an NMR tube with some compatible deuterated solvent (for locking)
3) Take the NMR spectrum and export the JCAMP-DX file (on our machines these are in a compressed format)
4) Open the initial JCAMP-DX files in JSpecView and save as JCAMP-DX XY format
5) Upload the converted file to the ONSC server in the spectra folder
6) Fill out the requested information in the SAMS spreadsheet and you have the solubility calculation (first open the SAMStemplate and save as a copy with a new name)

We can now easily finish processing the backlog of measurements that the ONSchallenge participants have been obtaining and record them in the SolubilitySum spreadsheet for querying.

Chemistry in Second Life April 09 Talks

2009-04-29T16:03:28.533-04:00

Andrew Lang and I just did two presentation on applications of chemistry in Second Life.

The first was on April 24, 2009 at the "Virtual Worlds: Libraries, Education and Museums" (VW LEM) conference on Infotainment Island. The second was on April 29, 2009 at "Education Days" on Orange Island.

This was basically an updated version of the talk we gave at the ACS last summer. We showed how the ChemTiles and Spectral Games evolved from Second Life. That is interesting because usually Second Life applications are adaptations of projects initially conceived elsewhere.

As I mentioned previously, giving talks on Second Life or using some other form of tele-presence certainly has its advantages. It does not replace face to face interaction but I think people get a good idea of what we do and they can follow up later for more discussion or possibly even collaborations.

I enjoy presenting with Andy - we go back and forth depending on the content on the slide and when it is relevant Andy does a demo of how to rez a molecule right on stage. So far we have not had any technical problems with that and I think it drives home the message of how easy it is to use the orac rezzer.

The talk on Orange Island was recorded and I'll update a link to it here when available.

Is it becoming dangerous to NOT blog?

2009-04-28T09:38:55.450-04:00

It wasn't so long ago that the big discussion about scientists blogging was whether or not it would hurt your career. Granted, some the examples used involved personal content that would have been problematic on any platform. Still, many scientists chose to blog anonymously, even for the most uncontroversial scientific musings.

Recently I have noticed a change in the tone. The question doesn't seem to be "Is blogging bad?" anymore but rather "Is blogging a waste of time?". Often this involves the rather ironic situation of naysayers using a blog to express their opinion that blogging is a waste of time. There are many examples of this but a particularly controversial discussion took place on Nature Network recently.

And then yesterday I came across a particularly good example of why blogging is not a waste of effort. I was checking my Sitemeter referring links and found a few from Nature Chemistry. Unfortunately the article is toll access but I was able to get my hands on a copy. It was Michelle Francl's article about the history of the periodic table and all the creative ways that people have used to demonstrate order in the elements.

Michelle used my blog post about Andrew Lang's 3D representation of the periodic table in Second Life as a reference for this type of table. This is a very short (4 sentence) post but it has the key elements of a good reference - answers to who? what? and where?. That is enough information to visit the exhibit and contact the creator for a copy.

Now Andy and I are witing this up as part of a larger article on chemistry in Second Life (see draft here). If that article had been completed and published, it is likely that Michelle would have used that as a primary reference. But it can take a really long time for the journal publication process to reach completion. If I had not blogged this I am sure Michelle could have adapted her article and found another similar reference.

The point is that mainstream scholarship (Nature Chemistry is certainly an example of that) is able and willing to use Web2.0 references when these are the most appropriate.

There are very few examples of mindblowingly original ideas. People working in related areas tend to come up with similar ideas. In a world where any of your competitors can blog their ideas as soon as they think of them, hoarding ideas might be the more dangerous choice.

It doesn't matter what you think about the professional status of blogs. It doesn't matter most scientists don't blog. The only thing that matters is that at least one of your competitors is willing to blog their research and that the traditional journals in your field are willing to accept blog posts (and other Web2.0 publication formats) as valid references.

NASA Open Notebook Science Talk April 09

2009-04-16T19:59:20.398-04:00

On April 15, 2009 I had an opportunity to give a talk at the NASA Goddard Space Flight Center. I talked about Open Notebook Science and all of the Web 2.0 tools that we use to operate. There were no chemists in the audience but hopefully the overall patterns of how all the components interconnected made enough sense to be useful.I had a full hour so this talk is a pretty comprehensive summary of our projects, including the most recent work on the Spectral and ChemTiles games and the automated backing up of Google Spreadsheet documents and semi-automated solubility calculations using web services called from within Google Spreadsheets. All of this work was only possible because of Andy Lang's rapid development efforts. Tony Williams also assisted greatly with the Spectral Game.slidesWe had a very nice conversation over lunch with a few NASA people. I found it interesting that many apparently very different user environments (librarians, educators, molecular biologists, cosmologists, etc.) share very similar needs for Web2.0 technologies. For example delicious was lauded as a very convenient alternative to email for sharing content. The distribution of personalities seems to be similar everywhere: a few early adopters within a larger more skeptical population.After lunch Emma Antunes gave me a tour of the facilities. Despite the annoying rain to get between buildings, it was well worth it. Here are some of the cool things that I saw:An enormous room housing very large speakers for testing the effect of vibrations on spacecraft and equipment. Emma stands next to one of the several speakers.A huge centrifuge for testing the robustness of instruments. Emma said that they were able to put an SUV on there to how much force was required to tip it over.I saw one of the satellites for the Solar Dynamics Observatory under construction. The idea of this project is to use the different perspectives from satellites at different positions in orbit around the sun to calculate the direction of solar flares and other potentially detrimental activity on the sun.Next to the largest clean room in the world, there is a display of the guts of the Hubble telescope. Apparently the astronauts had to fix some components in there that were not designed to be accessible so they had to do a lot of practice on a duplicate before attempting the task in space.[...]

Automatic Back-Up of ONS files: Google Spreadsheets, JCAMP-DX, Flickr

2009-04-12T22:06:14.710-04:00

As many of you know, we have been heavily dependent upon publicly editable Google Spreadsheets for storing results and calculations relating to our Open Notebook Science projects. We have recently integrated automated processing of NMR files in JCAMP-DX format to calculate solubility data by using web services called directly from within the Spreadsheets.That represents a lot of distributed technology that is susceptible to network or server problems. Andy Lang, who wrote the web services that currently calculate the solubility, has enabled the recall of previously calculated values via a quick database look-up. While this substantially reduces server load by avoiding lengthy calculations, it does mean that the final numbers do not exist in the Spreadsheets themselves.In addition to these concerns, every time I give a talk to a group of librarians the issues of archiving and curation of new forms of scholarship are raised. These are valid concerns and I've been trying to work with several groups to deal with the problem in as automatic a way as possible.We had initially considered a spidering service that would automatically follow every file linked to the ONS wikis and download the documents on a daily basis. This has turned out to be problematic because many of the links don't terminate directly on files, but rather user interfaces. For example, a typical link to a Google Spreadsheet does not lead to a simple HTML page that can be copied but rather to an interface to add data and set up calculations.It turns out we can take a semi-automated solution that gets us to where we want to be but requires a bit more manual work. Google Spreadsheets can be exported as Excel spreadsheets, which store the results of web service calculations as simple values and include the link to the web service as a cell comment. All calculations within the Spreadsheet are also retained in this way. The trick is to "publish" the spreadsheet using the advanced option of exporting as an Excel file. This then becomes a simple URL.Now, the only manual step left in the process is to copy these URLs to another BackUp Google Spreadsheet. Andy has created a little executable that steps through a list of these URLs and creates a backup on any Windows computer under a C:\ONS directory. It is simply then a question of setting up a Windows Scheduler service to run once a day and call the executable. All the files are named with the date as a first part of the name for easy sorting.Besides Google Spreadsheets backed-up as Excel files, spectral JCAMP-DX files and Flickr images can be processed in the same way. In both these cases the user must specify the JDX or DX or JPG file directly. In Flickr you have to go through a few clicks to the download page for a given image but once you have that it works fine.Andy has versioned this as V0.1 for good reason. It does do exactly what we want but there are a few caveats:1) Any errors in specifying a file will abort the rest of the back-up. In future versions there would be tolerance for errors, with appropriate reporting of problems, perhaps by email.2) Files don't necessarily have the correct extensions. For example, backed up Wikispaces pages have to be renamed with an HTML extension to be viewed in a browser. Note that Wikispaces has its own sophisticated back-up system that will put the entire wiki with all files directly uploaded onto the wiki into a single ZIP file - in either HTML or WIKITEXT format. Of course this will not include files residing outs[...]

Is the Human Ego good for Science?

2009-04-07T08:47:42.220-04:00

I have just finished reading the fascinating book "The Emperor of Scent" by Chandler Burr. It starts off describing the world of perfume with a focus on Luca Turin, a man with the unusual talent of being able to review perfumes with great eloquence, conjuring up beautiful metaphors of experiencing their scent. The book then takes an unexpected turn into the description of Turin's theory about the mechanism of olfaction. There is some truly interesting science there, such as Turin's discovery of a binding site for NADPH and another for zinc on a protein thought to mediate smell. This supports his hypothesis that the protein functions as an electron tunneling spectroscope detecting differences in vibrational modes. Further evidence is provided by comparing the different smells of deuterated molecules like acetophenone and the similarity of the stench of boranes with thiols, which share similar IR spectral bands. This idea is at odds with the conventional view that molecular shape is responsible for the activity of odorants. (For a summary of Turin's theory I would suggest watching his recent TED talk "The Science of Scent" and his Wikipedia entry)This is all very interesting stuff and would have made for a good read but what makes this a truly fascinating story is that Burr spends the rest of the book detailing the way the scientific community responded to his findings. As Turin waits a year to finally get rejected by Nature, the reviews, rebuttals and other communications with the editor are examined to expose the intense emotional components that can arise from the peer review process. The author even follows Turin to conferences and reports in detail how various members of the audience react and comment during his talk and at informal meetings over lunch. People who are not in science may find this disturbing. All too often science operates like the judicial system, where winning can take on more importance than finding the truth. The fundamental problem is conflict of interest. If you have patents or run a company it may not in your financial best interest to look under every rock, except as required by law. If you have built your career on a certain theory it may not be in your professional best interest to open every can of worms. Burr actually wrote a chapter explaining why the book appeared to be so one sided: it was hard to get detailed comments from Turin's detractors because, although they disagreed with his theory, they had not read his paper and did not have time to do so.But Turin was really not that different in his conflict of interest related to ego. There are descriptions of him reading articles in a state of dread and delaying experiments for fear that he might be proved wrong. Still, I like to root for the underdog, so the book did have me hoping that he would be vindicated.If most scientists are motivated by ego, is it possible to do egoless science - and what would that look like?For starters I think that keeping a true Open Notebook (All Content shared Immediately) does a lot to keep your ego in check. If you report on what you find, when you find it, you don't have time to succumb to the temptation to cherry pick results and embellish the story of what happened. Another trend that I think will emerge in the next few years and will change the way science gets done is machine-driven science. It will probably prove too much trouble to take into account a researcher's ego and career objectives when coding for AI to plan and[...]

The ChemTiles Game

2009-04-02T16:42:04.206-04:00

In another example of code and content re-mixing for educational purposes, Andrew Lang and I have adapted many of the elements of the Spectral Game and tiles from the Second Life quizzes I traditionally gave for my introductory organic chemistry course. Many of these tiles were originally created for use in Unreal Tournament.

The concept is simple: tiles represent images or statements that are either true or false in any context. By marking them as true or false and ensuring that one true tile is present in a mix of a number of false ones, games can be designed that vary from rooms within a maze to obelisks offering a selection of floating images in Second Life.

In the current implementation, the tiles appear in a web browser. Clicking on the correct tile produces a new random selection. Clicking on a false tile stops the game and records the player's score. Following the same structure as the most recent implementation of the Spectral Game, the first 10 queries present only two tiles. As the game progresses the difficulty level increases and more tiles are included.

Whereas the Spectral Game obtained spectra and molecules from ChemSpider, this game taps into a set of 256 x 256 pixel images in a Flickr group. Using Flickr lets us leverage the ability to easily tag images, which can then be used by players to select different topics to practice.

I'll be giving a prize to the student in my current CHEM241 class who scores highest by 10:50 ET April 10, 2009. The student must play under the "all tags" option, which covers all the material before test 1, given the following week. Students can also practice different modules by selecting tags like Lewis Structures, Hybridization, Nomenclature, Newman Projections, etc.

I think that this approach of rapid remixing of code and content on free hosted platforms (like Flickr or ChemSpider) is really the future of technology in education. It will be difficult for heavy top down - and expensive - systems to compete against the incredible flexibility of these lighweight and loosely connected initiatives led by educators with the simple motivation of just experimenting with teaching in a better way.

My Open Notebook Science talk at NASA in April 09

2009-04-02T14:15:17.555-04:00

I will be speaking at the Goddard Space Flight Center at 11:00 on April 15, 2009. NASA has a long history of sharing data and it will be interesting to see how their experience compares with what we have been doing in chemistry. Certainly the much larger amount of telescope generated data presents different problems and opportunities.

Crowdsourcing solubility measurements using Open Notebook Science

Jean-Claude Bradley

The use of Open Notebook Science to collect and make publicly available non-aqueous solubility measurements will be described. This involves the real time sharing of all experiments and associated raw data by a community of collaborators who are geographically distributed and may have never communicated using channels other than this project. Monthly cash prizes are awarded to participating students by means of the ONS Challenge Submeta Awards. The laboratory notebook pages are recorded on a public wiki and the solubility measurements, including relevant calculations, are stored in public Google Spreadsheets. A combination of ChemSpider, the GoogleDoc visualization API and web services is used to enable flexible searching and display of desired subsets of the data.

Tim Bohinski is the April 09 Submeta ONS Award winner

2009-04-02T08:47:42.096-04:00

Tim Bohinski, a Chemistry undergraduate student working under the supervision of Jean-Claude Bradley at Drexel University, is the April 2009 Submeta Open Notebook Science Challenge Award winner. He wins a cash prize from Submeta.

Tim mainly focused on evaporation techniques to measure solubility. He also wrote a review paper on non aqueous solubility. See his experiments here:
http://onschallenge.wikispaces.com/list+of+experiments

Five 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:
http://onschallenge.wikispaces.com
http://onschallenge.wikispaces.com/submetaawards08