Category Archives: Open Science..all its forms

Accessing 3D Printable Chemical Structures Online at #ACSsanfran

This presentation was given by Vincent Scalfani and covers the work we have done to provide access to 3D printable chemical structures online…

Accessing 3D Printable Chemical Structures Online

We have been exploring routes to create 3D printable chemical structure files (.WRL and .STL). These digital 3D files can be generated directly from crystallographic information files (.CIF) using a variety of software packages such as Jmol. After proper conversion to the .STL (or .WRL) file format, the chemical structures can be fabricated into tangible plastic models using 3D printers. This technique can theoretically be used for any molecular or solid structure. Researchers and educators are no longer limited to building models via traditional piecewise plastic model kits. As such, 3D printed molecular models have tremendous value for teaching and research. As the number of available 3D printable structures continues to grow, there is a need for a robust chemical database to store these files. This presentation will discuss our efforts to incorporate 3D printable chemical structures within the Royal Society of Chemistry’s online compound database.



Current Initiatives in Developing Research Data Repositories at the Royal Society of Chemistry

I presented at the Food and Drug Administration today regarding some of our efforts to develop a research data repository for the community. The abstract and presentation from Slideshare is below.

Current Initiatives in Developing Research Data Repositories at the Royal Society of Chemistry

Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. RSC hosts a number of chemistry data resources for the community including ChemSpider, one of the community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this cheminformatics platform and the nature of the solutions that it helps to enable including structure validation and text mining and semantic markup. ChemSpider is limited in scope as a chemical compound database and we are presently architecting the RSC Data Repository, a platform that will enable us to extend our reach to include chemical reactions, analytical data, and diverse data depositions from chemists across various domains. We will also discuss the possibilities it offers in terms of supporting data modeling and sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community.


Providing support for JC Bradleys vision of open science using RSC cheminformatics platforms

This presentation was given at the JC Bradley Memorial Symposium on 14th July 2014

Jean-Claude Bradley had an incredible passion for providing open science tools and data to the community. He had boundless energy, no shortage of ideas and ran so many projects in parallel that it was often difficult to keep up. But at RSC we tried. We provided access to our data, our application programming interfaces and lots of our out-of-hours time to help turn his vision into reality. As a result we helped in the delivery of the SpectralGame to help people learn about NMR and we supported the integration of our services into GoogleDocs underpinning the management and curation of physicochemical property data. We tweaked a number of our services based on JC’s input and as a result we have ended up with a suite of capabilities that serve many of our existing efforts to integrate to electronic lab notebooks and support the ongoing shift towards Open Chemistry. JC was very much ahead of his time….and we were glad to have supported his work. This presentation will give a snapshot of some of the work we did to support his vision.


A Photo Loop of Jean-Claude Bradley for the Bradley Symposium

On 14th July 2014 a memorial symposium to celebrate the life and work of Professor Jean-Claude Bradley, the father of Open Notebook Science, used this photo loop to connect us to some of his activities and give us a glimpse into his personal life.




Intention, collaboration, trust and willingness builds the JC Bradley Memorial Symposium

Next week I am looking forward to co-hosting the JC Bradley Memorial Symposium. How did this come about? The symposium is of course catalyzed by the tragic loss of our friend and colleague Jean-Claude. This hit Andy Lang and myself very hard (and of course many others) because for a number of years we had been collaborating together on a number of projects regarding Open Science, many of these to be discussed in some detail next week at the symposium. When we talked and discussed about ways to memorialize JC we happened upon an instance where we would both be in the UK at the same time and, since JC had so many interactions in place with European scientists and advocates for Open Science, we decided to try and make a go of a symposium to celebrate his work.

We received general support for a gathering and went seeking a venue that would be kind enough to host us. Thank you so much to Christoph Steinbeck for trying to make this work at EBI but because of the popularity of the venue no rooms were available. We extended our hand to Bobby Glen at the University of Cambridge and, gentleman that he is (!), he immediately gave us a home for the gathering. Bobby is Director of the Unilever center of molecular science informatics at the university and may well known scientists and open science evangelists work there, one of these of course being Peter Murray-Rust. Peter threw his support behind the symposium 100% and, together with Susan Begg, has taken all responsibility for local coordination. Despite Peter’s demanding travel schedule we have been able to coordinate the event and we owe a debt of gratitude to Susan for all the work she has done in the background to bring this together in such a short time. Literally, this event will come together as a result of a few skype calls between Andy and I and a series of email exchanges between us, Peter and Susan. When the event comes together, starting Sunday evening with a social gathering, and finally on Monday morning when the formal gathering kicks off, then intention, collaboration, trust and willingness to get it done will be the underpinnings of the meeting.

“Intention, collaboration, trust and willingness to get it done” speak volumes regarding how JC Bradley approached science. He was a get-it-done type of guy. The speakers that will gather next week, listed here, operate in the same way in my mind. They are driven, passionate and getting it done. We thank every one of them for taking their time to come and celebrate JC.

The gathering will honor his work and enormous contributions to open science. He was ahead of his time. With this gathering of people, and the support of the attendees, we hope that we will be able to discuss how to drive forward what he had put so much effort into…OPEN NOTEBOOK SCIENCE. Peter Murray-Rust has already outlined his thoughts and will expand at the gathering. What we will need to do is consider how to turn discussions into actions and deliverables to get it done. The symposium will be a start…the “networking events” (call them pub gatherings) will continue the discussions and what we do afterwards makes it work. Hope to see you in Cambridge!!!

For those of you who CANNOT attend on Monday of next week….you can still contribute…

If you have any photos of JC please send them through to me at tony27587ATgmailDOTcom for a photo loop

If you want to send a dedication to JC send a few words that I will show on a dedication loop sometime during the meeting.






Give me KUDOS for my articles

Over the past few years I have learned how to use a lot of the social networking tools and platforms to host and share my publications (when I am allowed to), my presentations, videos etc. I have started using a new website,, to help me enrich, expose and measure my publications. This is VERY EARLY in my exposure and usage of the platform but I am already excited by the possibilities. I applied KUDOS to one of the articles I co-authored with Sean Ekins and Joe Olechno regarding “Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses“. With almost 10,000 views it has become a very interesting article and has been discussed many times so there was a lot of online information to enrich the article with. The resulting KUDOS page is here:

Slideshare Article

Youtube Video


In Memory of Jean-Claude Bradley

My friend Jean-Claude Bradley was a dreamer. To lose him is a nightmare, a tragedy ….

My friend JC Bradley - leader, evangelist and practitioner of Open the max.

My friend JC Bradley – leader, evangelist and practitioner of Open Science…to the max.

When I received the sad news that JC had passed I went into the sad, dark place that losing family and friends sends me. And I went there fast. As we age we all need to face the challenge of increasing loss around is inevitable. And in recent years it is with increasing frequency. In two weeks time I turn fifty years old and for sure I am more conscious of my time on this planet than ever. My priorities have shifted over the years to more balance between life and work, WAY more quality time with the people I love and especially to my twin boys (while they still want me around!) and yet I am still driven to leave my mark in my domain of science. It doesn’t have to be dramatic, it doesn’t have to glorious…but I would like it to be catalytic and, hopefully, important. And someone pointing at it with a “Tony was involved with that”…will make me happy. Likely for less than a generation…but nevertheless. We should all be pointing at JC and LISTING the “JC was involved with that…”. I believe it would make him happy.

JC Bradley did something important. He did something catalytic. Actually he did a lot that was important and catalytic. And even though he has gone he will not be forgotten by his peers, his collaborators and his followers for a long time. And I believe his legacy will survive and flourish. JC was, for me, and many others, the father of Open Notebook Science. Fortunately he is remembered in this way on Wikipedia as coining the term.

I first met JC as a PhD student while I was at Ottawa University. I used to run 2D NMR for him in the days when walk-up 2DNMR wasn’t available….300MHz XL-300 Varian instrument. The good old days. We used to spread out spectra on the floor of my apartment and assigned data. Many a long night. Even then it was clear JC was a character…an interesting character. Driven. Focused. Serious..about his science. With a laugh for all the right reasons.

I lost track of JC until he got to Drexel but since we reconnected we have spent many, many long hours on phone calls, worked on many projects together for the sake of Open Science, and I have sat and laughed and visited the many trials and tribulations of openness with JC and people including Cameron Neylon, Andy Lang and many others. JC was driven, he was humble, he was a doer. He challenged the status quo with the spirit of a change agent but without the arrogance and brutality of some in the world of openness in chemistry.

I am not going to belabor the contributions he has made to Open Science. Many others will do that in the next few days. I will do it in presentations and in my writings for sure. His legacy will live on. For now I am going to grieve the loss of an evangelist, a driven practitioner in the world of Open Science, a humble man and my friend.

He traveled the world of Second Life while here  and wherever he is now, and I am making no judgments of peoples views of where that might be, I hope Horace Moody, the cat JC was in Second Life, is purring somewhere. In my head he is smiling, he is purring and he is proud. He should be. As Mays tells us….it is a calamity not to dream…and JC did….

“The tragedy of life doesn’t lie in not reaching your goal. The tragedy lies in having no goal to reach. It isn’t a calamity to die with dreams unfilled, but it is a calamity not to dream. It is not disgrace not to reach the stars, but it is a disgrace to have no stars to reach for.” -Benjamin E. Mays (American educator, Clergyman, 1895-1984)-


The Importance of the InChI Identifier as a Foundation Technology for eScience Platforms at the Royal Society of Chemistry

This is a presentation I gave today at Bio-IT 2014 here in Boston. I was in the company of a number of my favorite people to be o the agenda with… Steve Heller, Steve Boyer, Evan Bolton and Chris Southan.

The Importance of the InChI Identifier as a Foundation Technology for eScience Platforms at the Royal Society of Chemistry

The Royal Society of Chemistry hosts one of the largest online chemistry databases containing almost 30 million unique chemical structures. The database, ChemSpider, provides the underpinning for a series of eScience projects allowing for the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it specifically in the ChemSpider project to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a Global Chemistry Network encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.


The potential benefits of making yourself visible online as a scientist

The potential benefits of making yourself visible online as a scientist

This is a presentation I gave at MIT to the Boston ACS Young Chemists regarding how they can take advantage of some of the online tools to spread the message about their activities, their interests, get engaged with collaborative science and participate now to gain benefits from the growing world of AltMetrics


Digitizing documents to provide a public spectroscopy database

This is my sixth presentation at the ACS Fall Meeting in Indianapolis:

Digitizing documents to provide a public spectroscopy database

RSC hosts a number of platforms providing free access to chemistry related data. The content includes chemical compounds and associated experimental and predicted data, chemical reactions and, increasingly, spectral data. The ChemSpider database primarily contains electronic spectral data generated at the instrument, converted into standard formats such as JCAMP, then uploaded for the community to access. As a publisher RSC holds a rich source of spectral data within our scientific publications and associated electronic supplementary information. We have undertaken a project to Digitally Enable the RSC Archive (DERA) and as part of this project are converting figures of spectral data into standard spectral data formats for storage in our ChemSpider database. This presentation will report on our progress in the project and some of the challenges we have faced to date.