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Useful ChemistryUpdated: 2008-07-03T05:53:43.914-04:00 | ||
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Post Comments 2008-07-02T14:37:34.387-04:00 Update: the presentation videos are now available here.I'm back from the UCSD workshop on New Communication Channels for Biology held June 27-28, 2008. The first day mainly consisted of talks while the second was very heavy on breakout sessions (see agenda). Probably the most beneficial part for me was seeing old friends or meeting in person several people I had only interacted with online previously. For example was nice to finally meet Dan Gezelter from the OpenScience project and Hilary Spencer from Nature Precedings. I also had a blast over enchiladas on Friday night with Mike Nieslen and Jen Dodd. Mike gave a very engaging talk on the Future of Science on Thursday night. The presentations were recorded and should be available within a week on the wiki link above - I'll post an update here when I am made aware of it. The take-home message for me resonated around the idea that there exists a group of really strong advocates for the Open Science movement. The actual tools, whether they be wikis, blogs, custom databases or open-source software, were secondary to the fundamental philosophy of openness. The SciBarCamp breakout sessions were certainly very lively. Since we were mainly preaching to the choir, controversy was at a minimum. However we did acknowledge the difficulty in pursuing an Open Science agenda within the current establishment. It was hard to resist pointing out the remarkable recent success of FriendFeed in facilitating communication between life scientists. Of course Deepak brought that up during his session. The fact that this conference was organized and funded on such short notice is a testament to the commitment of the core Open Science group - thanks to John Wooley and Srikrishna Subramanian for making it happen! 
Post Comments 2008-06-23T18:06:22.421-04:00 Timo Hannay asked me to help with establishing a Second Life presence for the upcoming SciFoo meeting August 8-10, 2008. I think that a poster area in the style of SciFoo Lives On would work well.To kick things off, 23andMe will be presenting tomorrow June 24, 2008 at 10:00 PDT / 13:00 EDT/ 17:00 GMT on Second Nature island. Berci Mesko had already made arrangements for them to speak - and since they will be at SciFoo this is a convenient way to get things started. Other SciFoo presenters coming soon... The presentation area is next door to the SciFoo Lives On section: SLURL 
Post Comments 2008-06-23T16:40:10.890-04:00 My interview is now available on the ITConversations podcast. Jon Udell did a great job of covering lots of territory:
Post Comments 2008-06-23T11:01:10.635-04:00 I'll be attending the "New Communication Channels for Biology" Workshop at UCSD on Wednesday. It looks like it will be very intense and I hope to see a few people from the Open Science movement there!The workshop will focus on the range of emerging approaches within e-science, community engagement in dialogue knowledge input/review or assessment, science blogs, and authenticated wiki-like research discussions and analysis, as well as the potential to formalize such community level contributions. These new approaches to communication are becoming important for biology as biological scientists attempt to address the inherent complexity of life, manage both high information content and high throughput data streams, and employ the opportunities emerging from advances in e-communication/networking and information technology. In part, this meeting has been stimulated by the success of the PSI KB Annotation Workshop, and by the general need within research both in metagenomics and structural genomics to understand the changing means of scientific communication and how we can best reach out to the community and have our work be enhanced in timely impact. The general case of getting input to genomic data from the entire community, third party annotation and not from only the original provider, is another driver for the need to extend communication beyond traditional publications, but the transformations in scientific dialogue / communication are much broader than just that within the genome community.
Post Comments 2008-06-23T06:23:58.142-04:00 Tom Osborne from Mettler-Toledo will give a talk on laboratory automation at 10:30 a.m. on Tuesday July 1, 2008 in Disque 109 (32nd and Chestnut streets). The presentation will focus on chemistry applications of the MiniBlock, MiniBlock XT, and MiniMapper systems, including some results from the Bradley lab on the optimization of the Ugi reaction. A laboratory demonstration will follow in Disque 511. RSVP Jean-Claude.Bradley@drexel.edu to attend. MiniBlock® is a flexible, easy to use tool designed for parallel synthesis. MiniBlock® is the only compact parallel synthesizer that allows synthesis via Solid Phase or Solution Phase to be carried out on the same platform. Originally designed by medicinal and combinatorial chemists at Bristol-Myers Squibb Company, the MiniBlock® has been further developed to address a wide range of chemistry methodologies. 
Post Comments 2008-06-15T06:12:37.194-04:00 After receiving the MiniMapper two weeks ago we now have some numbers to look at from Trial 1.The idea here was to repeat a Ugi reaction known to work in methanol at 0.5M concentration (EXP099) and explore the experimental space varying solvent, concentration and an excess of some of the reagents. All 48 reactions gave precipitate (EXP189). We still have to optimize the lighting and camera angle to see this clearly for all tubes:  In reviewing the results I noticed an inconsistency between the experimental design and the information in the GoogleDoc used to plan the details of the experiment. But because the MiniMapper stores the log of its actions in an XML log file, Khalid was able to make corrections to the worksheet.Based on the weight of product and the limiting reagent, a yield for each reaction was calculated (column AC). The best 4 yields (48-61%) were found for 4:1 acetonitrile/methanol solutions at the lowest concentration (0.1 M). It is counterintuitive that a multi-component reaction should work better at lower concentration but this is an effect that I noted previously. Ironically, the absolute lowest yield (1.4%) was found for the 0.5M methanol reaction that was supposed to be the positive control! This may be due to a malfunction in the delivery of one of the reagents. However, the other reactions carried out at this concentration in methanol were all low yielding (10-15%), compared to when it was run manually in EXP099 (37%). I must stress that these results are very preliminary since we have not yet shown that the isolated materials are all pure Ugi products. As the NMRs come in I'll update the status. But I think that this was a good first trial to demonstrate what kind of questions can be asked with the power of automation and the importance of reporting automated logs in Open Notebook Science.
Post Comments 2008-06-11T05:53:58.892-04:00 The unveiling of Resident Chemist Andra Renard’s Amino World Exhibit is taking place today on ACS Island!Andra (Kenyon College biology professor Joan Slonczewski in real-life) and her assistant, Daniel, will be voice-enabled and accepting questions via text. The unveiling will be at 12 Noon PDT (SL time)/ 15:00 EDT on Wednesday, June 11, at http://slurl.com/secondlife Read more about it on the ACS blog.  
Post Comments 2008-06-10T14:30:23.226-04:00 Mat Todd reports on the Synaptic Leap:We've been successful in securing a large government grant with an open source component. The 3-year project concerns the enantioselective synthesis of PZQ for a low price, with the World Health Organisation as partner. (PDF of the Uni Sydney outcomes is here). The funding comes from the Australian Research Council (the main government funding agency in Australia). We wrote the proposal emphasising the possibilities inherent in the open source approach to doing science, and we're very pleased that this was seen as positive by an official grant-funding agency. The funding will allow us to increase our efforts on using TSL to drive our project forward much faster.
Post Comments 2008-06-07T06:31:54.581-04:00 Richard Stephenson from Southampton University has kindly added Drexel to their eCrystals X-Ray crystal structure repository, now located at: http://ecrystals.chemistry.drexel.edu Since we are operating under Open Notebook Science conditions, all of our structures will be made immediately available. However, the system is designed to allow contributors to select an embargo date if desired. Anyone from the Drexel community is welcome to participate. For example, the record for one of our anti-malarial compounds UC-150D can be shared through a simple URL: http://ecrystals.chemistry.drexel.edu/1. The 3D structure of the molecule is displayed in an interactive Jmol JAVA applet with links to all the relevant raw data files. The record can also be cited with a formal author list, making it convenient to acknowledge our crystallography collaborator (Matthias Zeller) and students who contributed.  Note that the crystal structure file for this compound is also available on its ChemSpider entry. In a world of Open Distributed Science, redundancy is information's best friend.
Post Comments 2008-06-03T09:20:23.966-04:00 On Friday I submitted a proposal to the Gates Foundation's Grand Challenges Explorations:Creative, unorthodox thinking is essential to overcoming the most persistent challenges in global health. The first vaccines were developed over 200 years ago because revolutionary thinkers dared to try an entirely new approach to preventing disease.There is a 2 page limit so the proposal was painted in very broad strokes. Since Nature Precedings doesn't take proposals anymore, I just uploaded it to Noam Harel's SCIEnCE wiki. The core concept is leveraging crowdsourcing and Open Notebook Science to develop new anti-malarial agents. It is similar to the last NSF proposal I submitted, except that the purpose is squarely on drug development, which is not allowed for NSF funding. I also broke it down into short sections and contributed it to the Thoughtmesh project just to see how that works. 
Post Comments 2008-05-30T15:37:02.683-04:00 As I mentioned previously, Mettler-Toledo is giving us a trial with their MiniMapper/MiniBlock system. Tom Osborne was in my lab yesterday to set it up. We got as far as setting up the software to recognize the positions of bottles and racks and pumping through some methanol. Once we're set up it looks like we'll be able to come pretty close to just copying columns from the Google spreadsheet of planned experiments to the MiniMapper software. This will make it very convenient for crowdsourcing Ugi experiments. Actually the worksheet for trial #3 is already set up to accept suggested experiments from anyone - no login required. Just note your name in the contributor column and put in a little explanation for your reasoning. For example, after looking at the master table of Ugi reactions, you may have a hypothesis that aromatic aldehydes lead to Ugi product precipitates at 0.5 M concentration in methanol. Just set up a dozen experiments probing that question. See the MettlerTrial wiki page for more info. I'll explain more about this later but if anyone wants to discuss collaboration contact me. We have the capacity of doing 96 experiments in parallel but Khalid will probably start with a dry run with pure methanol or a small section from Trial #1. Tom made a good point about how organic chemists need to think differently when designing experiments in parallel with automation. We have done parallel runs in vials but it gets tricky for people to keep track of everything. Machines are much better at this type of thing. You have to ask different questions when faced with 96 reaction tubes vs. a round-bottomed flask. And it looks like the MiniMapper software keeps a log in XML format - obviously more on that after our first trial...
Post Comments 2008-05-23T08:40:08.762-04:00 As Tony recently mentioned, there is a new button on ChemSpider to predict H NMR spectra based on the nmrdb.org web service: To give it a spin I am posting the experimental spectrum of Ugi product UC-150D underneath the predicted one.  This is going to be extremely helpful and yet another reason for using ChemSpider in active chemistry research. However, this tool does not replace the need for understanding how to interpret NMR spectra. First, two of the predicted peaks - the phenanthrene H at 8.5 ppm and the benzylic H at 5.7 ppm - are off by almost half a ppm. Second, the algorithm does not take into account the diastereotopic nature of the methylene group centered at 4.8 ppm. This is predicted to be a singlet but appears, as expected, as a pair of doublets. With this new tool there is a danger that students might think that they don't need to learn the finer details of NMR analysis since the predicted spectrum just pops up so conveniently. I hope people will report on what they find to be most and least reliable as they work on real problems. The beauty of ChemSpider is that both the theoretical and experimental spectra can be stored in the same record. Yet another reason to continue to routinely upload our spectra. Tag: InChIKey: PBZQTKRWYXTXIS-WLRTZDKTBU
Post Comments 2008-05-20T15:41:19.202-04:00 As I mentioned previously, one of the objectives of our research is to determine the conditions required for precipitation of pure Ugi products. Until recently, every precipitate we obtained could be characterized as the expected product.It looks like the situation is not so simple. For example consider Khalid's attempt (EXP171) to make Ugi product 171 H:  A nice precipitate was obtained...  But it does not correspond to the expected product. For one thing the tosyl group is missing - no non-exchangeable protons past 7.0 ppm. It clearly has the 3,5-dimethoxybenzaldehyde and possibly the methylamine and 2,4,6-trihydroxybenzoic acid components. It is insoluble in all common solvents except for DMSO. Although I'm not completely satisfied with the integration of the H NMR, the MS seems to match an iminium salt:  If this is the case it may be because of the significantly increased acidity of ortho-hydroxybenzoic acids. 2,6-dihydroxybenzoic acid has a pKa of about 1.5 (Papadopoulos 1991), compared with benzoic acid's 4.2 value. The problem may be with the isonitrile component TOSMIC. However, according to Chris Hulme, it should participate in Ugi reactions, even if it gives lower yields. We'll just have to do more examples and see if a pattern emerges.
Post Comments 2008-05-20T09:15:03.258-04:00 Antony Williams just published an article in Drug Discovery Today:Internet-based tools for communication and collaboration in chemistryThere is a detailed description of UsefulChem with a screenshot of EXP148 on Figure 2, where one of our Ugi products is characterized. This is another fine example of extensive interlinking between the worlds of peer-reviewed literature and Web2.0 content, including making use of Nature Precedings in the references.
Post Comments 2008-05-17T06:42:48.033-04:00 Kevin Owens and I have been looking into equipment to automate some UsefulChem experiments.This is something that I feel strongly will become important in Open Science applications, especially as it relates to Open Notebook Science. I think it is one of the paths of least resistance for the automation of the scientific process. Industry is automated to the gills but it will probably be easier to convince academic practitioners of Open Science to automate their procedures rather than to get industry to open their data. Can you imagine a company allowing crowds to design and analyze experiments run on their machines? That is what we've been proposing and it would be difficult to reconcile that with a business model based on IP protection. In that NSF proposal, we planned to use ChemSpeed's technology. Kevin and I recently visited ChemSpeed at their ChemSpeed's systems are quite powerful but also expensive (200-400K). In order to take advantage of more funding opportunities, we've also been looking at Mettler-Toledo's MiniMapper/MiniBlock solutions. We're planning this out openly on this wiki page - any feedback is welcome. I've had a good discussion with Frank Schoenen at the University of Kansas, where they run both systems as part of servicing the NIH Roadmap Program. Based on his feedback I think this trial run should be successful.  
Post Comments 2008-05-15T08:33:44.577-04:00 There has been a discussion recently on Michael Nielsen's blog about using a Google Custom Search for Open Notebook Science. Starting with UsefulChem, ChemTools (Cameron Neylon), OpenWetWare and Gus Rosania's 1CellPK, I created a search:http://tinyurl.com/4multu More sites can be added by volunteers. It will only work for sites that are accessible by a simple url (without a login). Give it a spin by searching "malaria" or "protein". We've already been using the Google Custom search for UsefulChem and it really works well - see the search box at the top of the UC wiki main page. It is also useful for teaching - for example to aggregate high level content about organic chemistry.  
Post Comments 2008-05-09T09:02:46.078-04:00 Just got my invite for SciFoo 08 (August 8-10) - I look forward to another intense meeting and catching up with friends and collaborators!Last year was truly enlightening. 
Post Comments 2008-05-07T13:16:06.233-04:00 Rodney B. Murray interviewed me last week for his educational podcast:
Post Comments 2008-05-05T11:26:09.325-04:00 I was asked by the Institute for the Future to highlight a dozen "Signals" that may point to new trends in science as part of the X2 Project:Today, science is entering another period of accelerated change, thanks to the growth of the Internet and dawn of pervasive computing; the explosive growth of new sciences like genetic engineering, nanotechnology, biotechnology, and simulation; the rise of new scientific powers in the developing world, the revival of amateur scientists, and the growth of citizen science movements in the United States and Europe; the growth of new institutions supporting scientific research and innovation, and changes in the structure and funding of universities, government, and corporate R&D labs. Science in 2025 and 2050 is going to look very different than it does today.Here are the 12 that I came up with:
Post Comments 2008-05-02T12:22:20.169-04:00 Earlier this week, I attended the LISE08 conference at the Chemical Heritage Foundation in Philadelphia. The theme this year was New Media and Technology in Science Education and I talked about using Second Life in the chemistry classroom.David Shaffer gave a very entertaining and thoughtful presentation on epistemic games. These are games simulating complex systems like urban planning. Tom Tritton reviewed the conference for CHF.
Post Comments 2008-04-27T13:52:02.569-04:00 As Antony Williams mentions in his blog, UsefulChem molecules now have their own url on ChemSpider:http://usefulchem.chemspider.com This is important on so many levels. I've been talking about using ChemSpider as an integral part of our research for some time now and we've been steadily migrating content as new functionalities became available. We still have a lot to do to complete the process but the path is clear. The ability to upload spectra of all types (IR, H NMR, C NMR, MS, etc) in JCAMP-DX format allows for anyone with a browser to drill down to any desired expansion using JSpecView. It just makes sense to upload the NMRs of our starting materials and our fully characterized products so that we can always be just a click away from the online lab notebook when discussing our chemistry. The value of being able do substructure searching for our compounds is immense. Most organic chemistry students are not interested in learning how to run and maintain software on a lab server to keep track of their molecules. They also don't want to learn SMARTS. ChemSpider has a very familiar graphic interface for drawing molecule fragments to do substructure searching. For a free and hosted solution, the energy of activation for using ChemSpider has become very low indeed, especially for Open Notebook Science applications. As we approach 200 experiments it is becoming clear that the ability to retrieve information is just as important as doing the experiments. Systematic tagging of experiment pages with InChIKeys and InChIs is a simple way to automatically allow for direct links from ChemSpider to UsefulChem pages via Google. We've come a long way from using a blog to track our molecules :) 
Post Comments 2008-04-18T06:29:46.558-04:00 The webcast from the Scholar2Scholar conference on April 16, 2008 is now available here. The general introductions start at 15:30, my intro by Jane Bryan starts at 19:08, my talk on "Enhancing Scientific Communication through Open Notebook Science" at 23:28 and the panel at 51:40 (after several minutes of dead audio unfortunately).The panel consisted of Jean-Claude Bradley, Andre Brown, Nicole Engard, James Mitchell, Banu Onaral, Beth Ritter-Guth, and Scott Warnock. Small round-table discussions followed and were diligently documented by the library folks. Their notes will be posted here on the wiki. Overall it was a very well organized and productive event. I was impressed by the level of engagement by the participants at my round table and I expect future projects to evolve from these discussions. I especially thank Jay Bhatt and Anita Chiodo for setting the process in motion a few months ago!
Post Comments 2008-04-17T17:18:20.634-04:00 Seema Singh wrote a review "India Takes an Open Source Approach to Drug Discovery" which just appeared in Cell: Volume 133, Issue 2, 18 April 2008, Pages 201-203. (The doi doesn't work yet but try this link in the meantime). You'll need a subscription to view it, an increasingly familiar irony of much of the Open Science discussion these days.UsefulChem and our collaborators got a nice mention: A related initiative is UsefulChem (http://usefulchem.wikispaces.com/), set up by Drexel University chemist Jean-Claude Bradley. Bradley has pioneered Open Notebook Science in which lab notebooks and raw research data are posted on the web for anyone to see and respond to (http://usefulchem.wikispaces.com/All+Reactions). As for success, Bradley says, “Probably the best example of a positive outcome from UsefulChem is finding two compounds that are somewhat active against malaria [in vitro],” blocking the activity of falcipain-2, a Plasmodium falciparum cysteine protease. “This demonstrates that a team of researchers can work together in the open—Rajarshi Guha from Indiana University did the docking calculations, my group at Drexel did the syntheses and Phil Rosenthal's group at UCSF did the testing.”
Post Comments 2008-04-15T20:40:30.578-04:00 Andrew Lang just finished coding this nifty little JCAMP-DX viewer in Second Life. The video shows that you can expand any area of the spectrum by typing zoom followed by the desired range in the chat box.You can also type "back" and "reset" commands. It essentially functions like Robert Lancashire's JSpecView if it were running in Second Life (although integration is not yet implemented). There are still a few kinks to iron out but it should work with any spectrum that can be represented in JCAMP-DX format: IR, CNMR, HNMR, UV-vis, MS, etc. This should extend considerably the set of tools available to chemistry teachers who use Second Life to interact with students. Give it a try on Second Nature island: SLURL. (You'll need the most recent version of Second Life to run this and click the link from within IE, not Firefox)
Post Comments 2008-04-15T20:11:52.444-04:00 The Scholar2Scholar conference is upon us. Jay Bhatt and Anita Chiodo did an amazing job with organizing this from the start. I'll be giving the introductory talk on "Enhancing Scientific Communication through Open Notebook Science". Here are the slides - I'm starting with an introduction to Web2.0 using FriendFeed as an example.date: April 16, 2008 8:30-1:30 location: Drexel University Bossone Lobby Join us to discuss how Web2.0 is changing scholarship. Dr. Jean-Claude Bradley will give a presentation, followed by a panel discussion featuring: Andre Brown, Nicole Engard, James Mitchell, Banu Onaral, Beth Ritter-Guth, and Scott Warnock. Small round-table discussions will follow. An optional Dutch-treat lunch concludes the day. 
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