Open Chemistry Presentation

Here is a link to a presentation on communication strategies of open chemists in comparison to traditional chemists.

EMBL Online Symposium

This should be of interest to anyone interested in scientific communication and Open Science:

Everybody with a scientific background is invited to participate. There is no registration fee payable. Have a look at our media to get an overview of the topics and speakers. Participating is quite easy: Please read the document in our info folder and make yourself familiar with the concept and conditions. After that you can create an account. Our media will be online starting from Monday, December 4 , 2006, 09:00 (CET). Until December 8 , 2006, 16:00 (CET) registered members can leave comments, discuss online and contribute with own content.

Thanks to Pedro for the link.

3QuarksDaily Series on Open Science

Bill Hooker just posted his second installment on Open Science.

In Part 1 of this essay, I gave an outline of the scholarly publishing practice/philosophy known as Open Access; here I want to examine ways in which the central concept of OA, the "open" part, is being expanded to encompass all of science.

It is a pretty thorough analysis of the various forms that openness can take in science. How nice that ONS is his favorite :)

My personal favourite (term and practice) is Open Notebook Science, but this seems better suited to being the name of the most open subset of Open Science practices since, as with Open Access, it is likely that a range of applications will co-exist and co-evolve.

His next post should also be of great interest:

...there will now be a third instalment. In that piece I will try to show what Open Science looks like now, in its infancy, and to sketch some of the directions in which it might grow.

Google Co-op for UsefulChem

You will notice a new search box on top of this blog. I finally got around to creating a Google co-op search site for all the websites related to UsefulChem. This includes all these:

• http://drexel-coas-elearning.wikispaces.com
• http://drexel-coas-elearning.blogspot.com
• http://usefulchem.wikispaces.com
• http://usefulchem.blogspot.com
• http://usefulchem-experiments1.blogspot.com
• http://usefulchem-molecules.blogspot.com
• http://showme.physics.drexel.edu/usefulchem

A lot of people have started doing (e.g. Sciencebase) this and I can see why. It works eerily well.

For example, searching for butylamine pulls up the correct UsefulChem page for t-butylamine. But the term "butylamine" does not appear anywhere on the page. Looking at the cache version in the results reveals that the term appears in a page pointing to this one. This thing is really smart!

There is really not much need anymore for using tables of content to navigate the knowledge space since this is so much faster. This is similar to how the speed and power of Gmail's search engine removes the need to file and sort emails.

Yet another reason why Google free services are likely to be a key component of the open scientific data revolution.

Youtube for test-tubes

The Journal of Visualized Experiments offers biologists the chance to observe the dissection of fruitfly ovaries without feeling too squeamish, find out exactly how to monitor actin disassembly with time-lapse microscopy, and even see how human embryonic stem cells are frozen for subsequent research. The science videos must save bio labs a lot of teaching time and costs for their grad student and post-doc training.

Is there an equivalent video system/journal for chemists? If not, there ought to be one. There must be dozens of standard procedures - drying reagents, vacuum distillations, separations, and syntheses - that could be recorded for posterity. Maybe the Useful Blogspot would be the place to start one...

By the way, JCB posted about this too.

Praise for OrgList

Although there has been a lot of attention lately on chemistry blogs, lets not forget about the old school technologies like mailing lists.

We have been having problems with the stink of gloves and glassware exposed to benzyl isonitrile that we use routinely in our Ugi reactions. Alicia posted this to OrgList and within minutes we got some great advice from Oliver Kern:

Best thing in my experience is to keep a bath of MeOH/conc.HCl(~2:1) in your fume hood and wash everything in that before you take anything out of the fume hood. An acid wash will destroy the isocyanides , i.e.hydrolyse them to the formamide or amine and thus eliminate the smell. Very occasionally you may find that you have leave things to soak in the bath over night - but usually this is not necessary. You'll find the more rigorous your wash and containment routine is with isocyanides the happier your lab-mates will be!

and from S.K.Adhikari:

All gloves, glasswares and contaminated materials can be conveniently dumped in a 10% aqueous solution of Ferrous Sulphate (commercial) kept in a HDPE drum. Keep for 10 mts, wash with water.Some suggest dil Hypochlorite ( but certainly I do not prefer )
You can test to satisfaction.

Try getting that from a commercial database or peer reviewed article!

JSpecView Demo

I spent some time today going over EXP042, the experiment done by Khalid and Lin recently to monitor by NMR the formation of an imine by mixing phenylacetaldehyde and t-butylamine in CDCl3. Since we have recently figured out how to save all of our NMR spectra in JCAMP format and view them using Robert Lancashire's JSpecView, I thought it would be a good idea to do a brief screencast demonstrating how this wonderful software can be used in a real chemistry experiment.

First I analyze the H NMR of phenylacetaldehyde and demonstrate the underintegration problem of the aldehyde proton. (Anyone out there know why the integral is only coming out to 0.65 H? This shows up in the printed spectra as well so it is not a JCAMP problem.)

Then I do expansions of the peaks that start to form 5 minutes after adding the amine. There is a triplet and a doublet with the same coupling constant that are consistent with imine formation. Finally, I show the mess that results after 42 minutes.

For more details read the discussion section of the experiment and please feel free to comment. To actually update the wiki directly just request an account. I don't allow anonymous guest updates because it is too easy for my students to forget to log in and I want to make sure they get credit for what they did.

I think this is a pretty good example of a "failed experiment" that would never be published to this level of detail by traditional publishers. How often do you get to do spectrum expansions even on supplementary data associated with a paper? I know that there are a lot of people doing Ugi reactions and the formation of the imine in some cases is apparently problematic. They can learn from what we have done and hopefully give a little back in comments from their own experience.

The video ipod compatible vodcast is available here.

Here it is on YouTube:

Wanted: Docking Collaborator

As pointed out by Peter and Joerg, the chemical blogosphere is getting more and more populated. This represents a great opportunity for collaboration. Indeed, there have been some examples of chemists asking for information and getting advice on blogs. Chemistry forums and mailing lists have served this purpose as well for some time.

In general it has been difficult for people to ask for a lot of information because of the fear of disclosing too much, I assume for patent and journal publication issues. Even with those concerns, the extent of the aura of secrecy is surprising to me. For example many chemistry bloggers still use pseudonyms, even though their content is high in quality and very uncontroversial.

In our research on the synthesis of new anti-malarial agents, we started with a list of 218 compounds that were predicted to dock with the parasite's enoyl reductase enzyme. Treweren, the company that ran the not-for-profit Find-A-Drug initiative, was kind enough to provide us with that list and the THINK software they used for the docking calculations.

As we are moving forward with the synthesis, we are finding that some analogues not in the original list but more accessible synthetically are worth investigating. Keeping with our Open Notebook Science philosophy, we are reporting these docking trials in wet experiment format with sections for Procedure, Results, Discussion, etc. For example, Sean reports on his investigation of certain THINK variables and the resulting docking energies.

The problem is that our expertise is in synthetic organic chemistry, not docking. This makes it very difficult to interpret our results with a great deal of confidence to decide if it is worth investing laboratory time and resources. What would be extremely helpful is feedback on how the calculations were done and how to interpret the results in a meaningful way. Or even better have some help with docking the molecules with a different program.

Basically I am asking for a collaborator who is interested in this malaria project and is willing to work openly. Any takers?

Copylefting Compounds

An interesting discussion about Open Source and Open Data in chemistry has popped up in the comments on a post on Egon's chem-bla-ics blog. It is important that we make our assumptions explicit when using these terms. Peter has taken the step of creating a Wikipedia entry for Open Data, providing a place for defining the terms we use. For example, I have added a detailed explanation of what I mean when using the term Open Notebook Science. When using the terms Open Source Science or Open Science in the past, I was pretty much using the definition I now use explicitly for ONS. It was confusing when people would use these terms but not provide any links to raw data.

In one of the comments, Peter notes:

In chemistry OD and OS (Bradley-like) overlap and are perhaps even synonymous. So in a sense Open Chemistry could be called simply OD. The added dimension in chemistry is the physical sample. Unfortunately the cost of transmission or replication is non-zero (unlike information and software). In some disciplines (e.g. microbiology) there is a real physical sharing of smaples (culture types). Does J-C have views on physical samples.

Although I have not really discussed physical samples in the context of ONS, under the description of our UsefulChem Molecules blog I state our policy:

We are happy to share compounds that we can spare, as long as their use is reported openly (including failed experiments)

This is similar to a copyleft policy, where creators agree to make their derivative works open as a condition of using documents and software. Of course in the case of physical samples there are costs associated with making the compounds and shipping but these are not excessive and we all stand to benefit if more researchers adopt this policy.

For those who don't wish to make their results public, we would consider selling some of our compounds to fund the lab. Some of these compounds are not commercially available yet and are useful for other applications. For example, DOPAL is an actively studied neurotoxin for dopaminergic cells.