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Category Archives: ChemSpider SyntheticPages

Personal experiences in participating in the expanding social networks for science

This is the third presentation I gave at the ACS Meeting in Indianapolis:

Personal experiences in participating in the expanding social networks for science

The number of social networking sites available to scientists continues to grow. We are being indexed and exposed on the internet via our publications, presentations and data. We have many ways to contribute, annotate and curate, many of them as part of a growing crowdsourcing network. As one of the founders of the online ChemSpider database I was drawn into the world of social networking to participate in the discussions that were underway regarding our developing resource. As a result of my experiences in blogging, and as a result of developing collaborations and engagement with a large community of scientists, I have become very immersed in the expanding social networks for science. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways that I expose my scientific activities online. Many of these activities will ultimately contribute to the developing measures of me as a scientist as identified in the new world of alternative metrics.

 

Navigating scientific resources using wiki based resources

Presentation given at ACS New Orleans Spring Meeting

There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.

 

Engaging students in publishing on the internet early in their careers

Presentation given at ACS New Orleans Spring Meeting

As a result of the advent of internet technologies supporting participation on the internet via blogs, wikis and other social networking approaches, chemists now have an opportunity to contribute to the growing chemistry content on the web. As scientists an important skill to develop is the ability to succinctly report in a published format the details of scientific experimentation. The Royal Society of Chemistry provides a number of online systems to share chemistry data, the most well known of these being the ChemSpider database. In parallel the ChemSpider SyntheticPages (CSSP) platform is an online publishing platform for scientists, and especially students, to publish the details of chemical syntheses that they have performed. Using the rich capabilities of internet platforms, including the ability to display interactive spectral data and movies, CSSP is an ideal environment for students to publish their work, especially syntheses that might not support mainstream publication.

 

 

Challenging cajoling and rewarding the community for their contributions to online chemistry

Presentation given at ACS New Orleans Spring Meeting

Chemistry online is represented in various ways including publications, presentations, blog posts, wiki-contributions, data depositions, curations and annotations. Encouraging participation from the community to participate in and comment on the information delivered via these various formats would likely provide for a rich dialog exchange in some cases and improved data quality in others. At the Royal Society of Chemistry we have a number of platforms that are amenable to contribution. This presentation will provide an overview of our experiences in engaging the community to interact with our various forms of content and discuss new approaches we are utilizing to encourage crowdsourced participation.

 

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BlogSyn – The Ongoing Pursuit of Blogging Chemical Reactions

There is a new “synthetic blog” online..this one is Blog Syn. The site has a declared focus listed as “….a new chemical literature review site. We
don’t just discuss the methods, we put them to the test!” This joins the other synthetic chemistry blogs such as TotallySynthetic and OrgPrepDaily. There are likely MANY others!!! What would be ideal is if these were to be aggregated in some way. For sure they are federated…you can consider that Google does that for you. But they are heterogeneous in format, very different styles and, in terms of the contribution to a contributors career, they may have less traffic on a blog than on a platform designed for the publication of syntheses.

Prior to joining RSC those of us running the ChemSpider website discussed setting up an environment for people to publish their syntheses. ChemSpider for compounds and ChemSpider “Reactions” for reactions. We chatted about it looking like a blog. We never started the project though as there were enough things to do. What we did release was the ChemSpider Journal of Chemistry that was more of an online journal.

When RSC acquired ChemSpider and we showed up in Glasgow for our first conference we discuss at that conference our old idea of a reactions type blog. What we talked about was that it would be a place to expose chemical reactions, for online comments and feedback and a place for a reaction to be DOI’ed and therefore of value to a resume. Since ChemSpider was very capable we knew there was a way to integrate spectral data, movies and other multimedia. We started considering the transfer of aspects of the ChemSpider journal of chemistry into a synthetic reaction platform. We realized that what we were trying to do had already been achieved by the SyntheticPages group. We chatted with the scientists involved with that platform and decided it would be best to bring our efforts together. And so we did….

The result is ChemSpider SyntheticPages (CSSP). The story of CSSP is described here in a discussion with Peter Scott of the CSSP Editorial Board.

CSSP is well established. Some of the authors have almost 90,000 page views. Spectra are embedded directly from ChemSpider into the page and chemicals are marked up and linked out to the relevant pages on ChemSpider. People are willingly adding their comments. The authors are DOI’ed. The platform has been around almost 10 years at this time…using SyntheticPages as the original seed set and adding articles directly to CSSP later. We are averaging < 10 articles a month though! Mostly that is because people do not know what it is. Last week I gave a talk in the UK and most people in the room have not heard of CSSP. But there it is…likely a near ideal platform for publishing syntheses online. We are recognizing contributors at present with labcoats as part of our initial rewards and recognition program and hope that recognition will encourage further participation.

We encourage you to look at platforms such as Blog Syn as well as CSSP and consider contributing your syntheses to these online platforms. They can be valuable hosts for your data. There will likely be more that show up as chemists recognize the value of exposing their data online!  It would be great if you consider fitting your synthesis into the homogenizing template of CSSP even if you publish elsewhere. It makes for a cleaner micropublishing platform overall we find. In any case…continue your online synthesis exposure!!!!

 
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Posted by on January 21, 2013 in ChemSpider Syntheses, ChemSpider SyntheticPages

 

A Hairy Christmas Story for the Holiday Season

As a scientist myself, and after years of pulling my hair out over various projects (as well as some of the conversations I have with my twin boys) there are times I wish that I wasn’t “thinning on top”. This video uses the holiday season to help encourage those of us who are “follicly challenged” to realize that science will give us the solution. This movie is a collaboration between my good friend Professor Alex Tropsha from the University of North Carolina in Chapel Hill (http://pharmacy.unc.edu/Directory/tropsha) and myself (Antony Williams, http://www.chemconnector.com/) where we did a few takes …literally 8 different shots only, in less than an hour. With a little bit of waxing lyrical to an old classical Christmas Song, and a quick self-training course in Microsoft Movie Maker (BRILLIANT SOFTWARE) I threw this together in about 2 hours. Enjoy! And there is hope for all us who, because of the excess heat from our skulls from “all that thinking”, are evaporating the follicles.

Please do note that Alex is modeling a ChemSpider SyntheticPages labcoat. Want to win one? Then you need to write a few articles here: http://cssp.chemspider.com/

I would like to acknowledge my mother for giving me a singing voice that sounds like I am gargling broken glass.

 
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Posted by on December 7, 2012 in ChemSpider Chemistry, ChemSpider SyntheticPages

 

ChemSpider Reactions – When Compounds are Not Enough

ChemSpider has become one of the worlds primary online resources for finding data, information, links, images, spectra..and on and on…about “chemicals”. Building a database of over 28 million chemicals that grows in some way in content, functionality and richness on a daily basis is, to say the least, a lot of work. But our cheminformatics team here at the RSC is not scared of work. We like it! So when we decided that it was time to enhance our efforts around the management of chemical reactions to move from ChemSpider SyntheticPages to a database of chemical reactions containing 10s if not 100s of thousands of reactions the question was how. What software platform would we use? Where would we source reactions? What functionality would we need to roll out as an early display of capability to entice users to test it out, give feedback and, ultimately, get involved. We made those decisions and we will be showing off the results of our project “ChemSpider Reactions Database” (yes, we’re very creative with our project titles aren’t we!!!) at the Fall ACS in Philadelphia.

If you want to learn what we are up to in regards to chemical reactions come and visit with us at the ACS booth…we’ll show an early view of over a quarter of a million reactions in an online, free to access database. We’ll chat about some of our future plans and hopefully engage you in a discussion about whether or not you would be willing to contribute reactions to the database. Wouldn’t it be good if we can provide to synthetic chemists a platform for accessing and managing reactions as we have done for chemicals. Of course, seamlessly integrated and platform independent…served up by the latest web technologies and mobile-enabled. What the future could look like… exciting times!

 

The Story of Olympicene from Concept to Completion

The story of Olympicene, and our intention to try and get it synthesized and analyzed, was first reported in August 2011 here. The original conversation was between Prof Graham Richards and I over a drink in Belgium at the RSC Editors Symposium in March 2010. The concept of having someone synthesize a small organic molecule that would be a molecular representation of a famous symbol of sport was a fascinating challenge. And, always one for a challenge, it was one that was pursued with great gusto!

Since we had started the ChemSpider SyntheticPages (CSSP) platform recently I thought it was appropriate to kick off a grand vision discussion with Peter Scott, one of the editors of CSSP. My original idea that I bounced off of Peter was a big one…an international competition exposed to the chemistry community. Encourage chemistry labs around the world to submit their step-by-step syntheses to CSSP. We would be able to collect and expose all of this work to the entire chemistry community. We would set up a voting scheme for the community to give their input on what was the most elegant synthesis, the greenest, what had the best analytical data, what had the best write up. Not all categories were detailed at that time and would come later but the concept of bronze, silver and gold medal winners in an international chemistry competition made sense. We were really excited by the possibilities but for many reasons (read that as many distractions) we rolled the announcement out as a smaller announcement and encouraged participation as best as we could with a small engagement profile via this blog. It did seem to garner a lot of attention but as is common with such projects the participation was not as high as we expected. Nevertheless one lab did step up to participate in the project, the lab of David Fox Group at the University of Warwick. David is a colleague of Peter Scott’s…small world…

David had one of his students pursue the synthesis, not only because the olympicene molecule might be an elegant piece of synthetic work, but also because some of the envisaged properties could well be of value (more on that later!). Anish started publishing his syntheses to CSSP in November of last year as listed here. You can see the Olympicene compound coming together step by step and yes, the final step is not yet reported! Once the compound was made then the possibilities of having it analyzed seemed rather interesting, especially having seen the work reported by IBM in 2009 regarding the single molecule imaging of pentacene. Also, I had followed the work of Marcel Jaspars, who I had known during my time working at ACD/Labs when I was working on Computer-Assisted Structure Elucidation [1,2]. Marcel had recently worked on an NMR and microscopy imaging project to confirm a chemical compound structure. Again, small world. I asked Marcel for an intro to the researchers at IBM and we started a dialogue. Researchers at University of Warwick had already applied Scanning Tunnelling Microscopy (Dr Giovanni Costantini and Ben Moreton at Warwick) and they then connected with Leo Gross with the idea of using the noncontact atomic force microscopy approach.

Within a fairly short period of time IBM had performed the very elegant work of imaging olympicene…just one of the images is shown below but there are others shown on the Flickr account.

A single olympicene molecule is just 1.2 nanometres in width, about 100,000 times thinner than a human hair. This is beautiful! For whatever reason it looks like a molecule with a smile at the success of the work too!

The story of the work is described in this video below.

The work is not over yet! There is a research paper to come from the University of Warwick and IBM Research labs as there is definitely unique science that has come out of this work and definitely needs to be reported. That molecule, as it were, is “NOT just a pretty face”. We will submit all the appropriate images and available analytical data onto ChemSpider and CSSP as time allows.

For now I simply smile at the story of a concept discussion between Graham and I that was taken into the hands of superb scientists and brought to fruition. Congratulations to ALL of those who worked on the project in David Fox’s and Leo Gross’s labs. Thanks to the marketing people at IBM, RSC and Warwick for bringing together all of the materials in a tight time frame to tell the story. My thanks to my colleagues at RSC who believed in the potential of this project and especially to Peter Scott for seeing the potential and willingly participating! This project is a great example of international collaboration and pushing science to its extremes. It was a pleasure to be involved if only at a concept level and HOPEFULLY I will get to meet the scientists who did the work sometime!

 

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