Defining the Future for Open Notebook Science – A Memorial Symposium Celebrating the Work of Jean-Claude Bradley

Cambridge University - Monday July 14, 2014.


Jean-Claude Bradley was one of the most influential open scientists of our time. He was an innovator in all that he did, from Open Education to bleeding edge Open Science; in 2006, he coined the phrase Open Notebook Science. His loss is felt deeply by friends and colleagues around the world.

On Monday July 14, 2014 we gathered at Cambridge University to honour his memory and the legacy he leaves behind with a highly distinguished set of invited speakers to revisit and build upon the ideas which inspired and defined his life's work.


This event was open and registration was free; 38 people were in the room. It was also streamed live, online and via the #jcbms hashtag there was significant participation on Twitter. 500+ tweets from 70+ accounts were collected in this archive, itself open source.


Simon Coles, University of Southampton, UK
Robert Hanson, St. Olaf College, USA
Nina Jeliazkova, Ideaconsult, Bulgaria
Andrew Lang, Oral Roberts University, USA
Daniel Lowe, NextMove Software, UK
Cameron Neylon, PLOS, UK
Peter Murray-Rust, Cambridge University, UK
Noel O'Boyle, NextMove Software, UK
Henry Rzepa , Imperial College London, UK
Valery Tkachenko , Royal Society of Chemistry, UK
Matthew Todd, University of Sydney, Australia
Antony Williams, Royal Society of Chemistry, UK
Egon Willighagen, Maastricht University, Netherlands


The location for the symposium is the Department of Chemistry, Cambridge University.
The program is now available (.pdf)

Sunday July 13
6:00 PM - Closing Time. Dinner and Social at The Anchor

Monday July 14
All of today's events will be in and around the Unilever Theatre, Department of Chemistry, Cambridge University.
9:00 AM - 9:20 AM
9:20 AM - 9:25 AM
Peter Murray-Rust
Welcoming Remarks
9:30 AM - 9:45 AM
Simon Coles
Inspired by Jean-Claude: Incorporating Electronic Laboratory Notebooks in Publications & Chemistry in Second Life
9:50 AM - 10:05 AM
Robert Hanson
Global Molecular Connectivity: The New "Model Kit"
10:10 AM - 10:25 AM
Nina Jeliazkova
On chemical structures, substances, nanomaterials and measurements
10:30 AM - 10:45 AM
10:50 AM - 11:05 AM
Andrew Lang
The Revelation of Jean-Claude Bradley
11:10 AM - 11:25 AM
Daniel Lowe
From Open text mining solutions to Open Data resources
11:30 AM - 11:45 AM
Cameron Neylon
Jean-Claude, the Overton Window, and the challenge of Open
11:50 AM - 11:55 AM
Peter Murray-Rust
Presentation of Blue Obelisks
11:55 AM - 1:25 PM
Lunch in the Unilever Centre
1:30 PM - 1:45 PM
Peter Murray-Rust
Open Notebook Science NOW!
1:50 PM - 2:05 PM
Noel O'Boyle
Chemistrifying the Web - Coupling Online Chemistry Resources for Education and Research
2:10 PM - 2:25 PM
Henry Rzepa
Opendata: The Student Experience at Imperial College
2:30 PM - 2:45 PM
2:50 PM - 3:05 PM
Valery Tkachenko
RSC Open Source Cheminformatics Platforms and Libraries
3:10 PM - 3:25 PM
Matthew Todd
Open Source Drug Discovery for Malaria
3:30 PM - 3:45 PM
Antony Williams
Providing Support for JC Bradley’s Vision of Open Science using RSC Cheminformatics Platforms
3:50 PM - 4:05 PM
Egon Willighagen
How I failed to do Open Notebook Cheminformatics
4:10 PM - 4:15 PM
Henry Rzepa and Peter Murray-Rust
Bradley-Mason Prize [NEW]
4:15 PM - 4:20 PM
Peter Murray-Rust
Open Notebook Science Initiative (Introduced by Peter Murray-Rust) [NEW]
4:20 PM - 4:30 PM
Antony Williams
Video Tributes & Closing Remarks
6:00 PM - Closing Time. Dinner and Social at The Anchor or Panton Arms


"Inspired by Jean-Claude: Incorporating Electronic Laboratory Notebooks in Publications & Chemistry in Second Life" - Simon Coles, University of Southampton
In memory of my colleague on the Editorial Board of Chemistry Central Journal, I will mark J-C’s commitment to Open Data in publishing by outlining some recent work published in the journal that demonstrates seamless linking from the paper to the source Electronic Laboratory Notebook for the work. J-C’s desire for scientific rigour in Open Notebook Science was exercised during the preparation and publication of this work! In the second half of my talk I will change tack and show some work on chemistry in Second Life which was conducted several years ago and inspired by J-Cs pioneering work in this area.

"Global Molecular Connectivity: The New 'Model Kit'" - Robert Hanson, St. Olaf College
The vision that J-C so vigorously promoted, of a world where chemical data is widely available and easily obtainable is becoming a reality. In this presentation I will show how recent advances allows Jmol to tap into resources around the world to seamlessly and almost instantly connect molecular names, structure, properties, and spectroscopy.

"On chemical structures, substances, nanomaterials and measurements" - Nina Jeliazkova, Ideaconsult
This talk attempts to highlight how I came to recognize the fundamental role of measurements, coming from the realm of data modelling and data analysis. Besides retaining the data provenance it provides insights how do we go beyond chemical structures and address the challenges of representing the identity of chemical substances and nanomaterials (with examples from the latest developments of AMBIT web services and OpenTox API). Finally, supporting the vision of distributed, open, web-like approach towards recording subtle experimental details is essential, not only for the chemists and biologists in the labs, but for all of us using, modelling, storing and querying the data.

"The Revelation of Jean-Claude Bradley" - Andrew Lang, Oral Roberts University
Jean-Claude Bradley blazed a trail that many of us have followed. A true visionary, a dreamer of dreams, but what was his motivation? What was the goal he was striving towards? What was his vision of the future and why was Open Notebook Science a part of that vision? I will present Jean-Claude's work, from coining the phrase 'Open Notebook Science' to his latest project 'Chemical Rediscovery,' through the lens of defining the future for Open Notebook Science. Presentation

"From Open text mining solutions to Open Data resources" - Daniel Lowe, NextMove Software
OPSIN (Open Parser for Systematic IUPAC nomenclature) has developed into a mature solution for chemical name to structure conversion. Together with other Open Source utilities such as OSCAR4, ChemSpot, and ChemicalTagger, we now have the tools to address many of the problems in chemical text mining. This ecosystem of tools has facilitated the extraction of over a million reactions, from the US patent literature, which are now available freely to all under CC-Zero. I will describe advances in OPSIN, how reactions can be extracted from text, and present some interesting analyses that are made possible by the public availability of this dataset.

"Open Notebook Science NOW!" - Peter Murray-Rust, University of Cambridge and Shuttleworth Fellow
Open Notebook Science can revolutionise science in the same way as Open Source has changed software. Its impact will be massive: greatly increased quality, removal of waste and duplication, and an inclusive approach to involving citizens in science. It's straightforward to do in many areas of science, especially computational. I shall present an ONS model which we can all follow and adapt. The challenge is changing minds and to do that we should start young.

"Jean-Claude, the Overton Window, and the challenge of Open" - Cameron Neylon, PLOS
Jean-Claude challenged us daily to meet a set of standards that all found difficult and some found exasperating. In holding us and himself to such high standards he consistently demonstrated what was possible. He moved discussion from what would be made available to what was too difficult (today) to make available, shifting the Overton Window on what "Open" really meant in the context of practicing chemistry. Today with Open Access and Open Data increasingly mainstream concepts - some would say appropriated and misused concepts - we need to both strengthen and question what we mean when we say something is "Open". Is our concept of Open, rooted as it is in a technological and western culture, even appropriate for the rest of the world. In many ways our conception of Open practice is rather passive - expecting that others will engage or utilise resources. I will argue that we need to have an active concept of Open, one in which community building is central, and we expect and welcome the way those communities will challenge our principles. If "Open" is built on the idea of a community of equals sharing resources then we need to actively engage with the reality that we are not equal, either in access, or control. What does this mean in practice as we try to realise Jean-Claude's vision? What are the standards and principles we need to keep challenging ourselves to move in the correct direction?

“Chemistrifying the Web - Coupling Online Chemistry Resources for Education and Research” – Noel O’Boyle, NextMove Software
Jean-Claude Bradley embraced online technologies as an enabler for improved collaboration, enhancing teaching through visualisation and interactive exercises, and as a bridge to link experimentalists to computational predictions. With examples from my own work and that of Jean-Claude, I show that thanks to the availability of online chemistry resources such as ChemSpider and the Chemical Identifier Resolver, there are many opportunities to add chemistry into common tools or software that can benefit teachers and researchers.

"Opendata: the student experience at Imperial College" - Henry Rzepa, Imperial College London
For six years now, we have introduced our undergraduate and postgraduate students to the experience of producing open data as part of their degrees. With the UGs, this is factored into their laboratory experiments, and with the PhD students into their theses. My talk will introduce some of the tools used to achieve this over this period. It will be illustrated with examples with a focus on computational chemistry in particular. Recent additions to these tools include new ways of factoring lecture notes into open interactive environments, persistent identifiers, DataCite, ORCID, the creative development of new styles of datuments by students themselves and how the impact of such open data publication can be measured. The presentation itself will be open, with identifier

"RSC Open Source Cheminformatics Platforms and Libraries" - Valery Tkachenko, RSC
The cheminformatics group at the Royal Society of Chemistry has supported a number of national and international grants for the last 5 years with the deployment of Cheminformatics tools and platforms. Among them is the Open PHACTS project which is intended to help reducing the barriers to drug discovery in industry, academia and for small businesses by providing the Open PHACTS Discovery Platform. The PharmaSea project targets the identification of leads for new antibiotics in deep sea trenches. The National Chemistry Database Service and Data Repository is a collaborative platform for handling research data. Our contribution to all of these projects has been the development of a number of open source cheminformatics library and user interface components that can be freely used in 3rd party websites and applications. In this presentation we will cover our approach to the development as well as give particular examples of applications built using our toolkits. These software components will likely be very important in the future deployment of Open Notebook Science platforms to help deliver on the vision of Jean-Claude Bradley.

"Open Source Drug Discovery for Malaria" - Matthew Todd, The University of Sydney
Some of Jean-Claude Bradley's earliest work in open science was directed at finding new molecules that could be used to treat malaria, one of the world's most deadly infectious diseases. This talk will outline the design and principles of Open Source Malaria, where all data and ideas are freely shared, anyone may participate at any level and there will be no patents. The open, meritocratic structure of the project has been essential in eliciting experimental contributions from around the world. Two molecules in the current series of most interest have shown high parasite clearance rates in mice, bringing closer the moment where we might see a public domain compound entering clinical trials.

"How I failed to do Open Notebook Cheminformatics" - Egon Willighagen, Maastricht University
I always believed that with Open Data, Open Source, and Open Standards I was doing the right thing; that it was enough for a better science. However, I have come to the realization that these features are not enough. Surely, they aid Open collaborations, though not even sufficient there, but they fail horribly in the "scientific method." Because while ODOSOS makes work reproducible, it lacks the context needed by scholars to understand what it solved. That is, it details out in much detail how some scientific question is answered, but not what question that was. As such, it fails to follow the established practices in scholarly research. In this presentation I will show how I should have done some of my research, and ponder on reasons why I had not done so.

"Providing Support for JC Bradley’s Vision of Open Science using RSC Cheminformatics Platforms" - Antony Williams, RSC
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.

Travel & Hotel Information

The department of chemistry at the University of Cambridge is located on Lensfield Road, Cambridge, UK. Location Map
There is no parking on site. Here's a Parking Map which shows details of parking in Cambridge. If you would like to make hotel reservations, we suggest you browse Visit Cambridge .


Cambridge had eduroam and we also pre-ordered tickets for the Cambridge network. Hashtag is #jcbms

Streaming and Recording

The meeting was streamed and recorded, thanks to Ron Haynes and Chris Chalk. There is a "virtual room" which you can visit. The streams include
  • relay of the screen
  • video of presenter
  • audio of room (I have not yet asked whether there will be microphones for the audience but it's a small room).

Meeting Name: Unilever Centre Lecture Theatre
Invited By: IT Support Chemistry
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Feel free to contact one of the organizers for more information: Antony Williams (tony27587<at>, Peter Murray-Rust (pm286<at>, or Andrew Lang (asidlang<at>


The University of Cambridge

ONS Inititiative

[PMR] Objective to create a paper/manifesto which explains/promotes/facilitates ONS
Edited communally , starting today... Everyone (literally) can contribute
Should be science in general.


General principles. Suggest extracting prose from (a) BOAI (?BBB) OA declaration (b) JCB's writings
(c) Bermuda Declaration


Collection of JCBs and Mat Todd's work

Fundamentals of ONS

Taken largely from JCB, but also maybe Michael Nielsen, Tim Gowers, GalaxyZoo.
"No inside knowledge", etc.


Quality of research
Cost-saving (not the primary one

Implementation - need for infrastructure (and funding)
6 laws of Open Source Malaria

Inclusivity of contribution
Collection of resources - individuals, univs, companies, governments

Where to start?
Everywhere. Stress the need to involve YOUNG PEOPLE everywhere