O'Really?

April 1, 2014

The Serene Scientists Serenity Prayer via Jon Butterworth

banksy church

The Church of Banksy

Whatever your religous preferences, the Serenity Prayer by Reinhold Niebuhr captures a certain wisdom about life in general. So it is good to see that physicist Jon Butterworth at UCL has adapted it [1] for scientists:

“Give me grace to accept with serenity the things that cannot be understood,

Data to investigate the things which can be understood,

And the Wisdom to know the difference.”

Amen!

References

  1. Jon Butterworth (2014) Giles Fraser says scientists are replacing theologians. Some thoughts on that The Gruaniad, 2014-03-31

February 18, 2013

August 20, 2012

Digital Research 2012: September 10th-12th at St. Catherine’s College, Oxford, UK

The Radcliffe Camera, Oxford by chensiyuan

The Radcliffe Camera, Oxford by chensiyuan via wikipedia

The UK’s premier Digital Research community event is being held in Oxford 10-12 September 2012. Come along to showcase and share the latest in digital research practice – and set the agenda for tomorrow at Digital Research 2012. The conference features an exciting 3-day programme with a great set of invited speakers together with showcases of the work and vision of the Digital Research community. Here are some highlights of the programme – please see the website digital-research.oerc.ox.ac.uk for the full programme and registration information.

New Science of New Data Symposium and Innovation Showcase  on Monday 10th: Keynotes from Noshir Contractor [1] (Northwestern University) on Web Science, Nigel Shadbolt (Government Information Adviser) on Open Data and a closing address by Kieron O’Hara (computer scientist) – with twitter analytics, geolocated social media and web observatories in between. Also the launch of the Software Sustainability Institute’s Fellows programme and community workshops.

Future of Digital Research on Tuesday 11th: Keynotes from Stevan Harnad on “Digital Research: How and Why the Research Councils UK Open Access Policy Needs to Be Revised” [2], Jim Hendler (Rensselaer Polytechnic Institute) on “Broad Data” (not just big!), and Lizbeth Goodman (University College Dublin) on “SMART spaces by and for SMART people”. Sessions are themed on Open Science with a talk by Peter Murray-Rust, Smart Spaces as a Utility and future glimpses from the community, all culminating in a Roundtable discussion on the Future of Digital Research.

e–Infrastructure Forum and Innovation Showcase on Wednesday 12th opens with a dual-track community innovation showcase, then launch the UK e-Infrastructure Academic Community Forum where Peter Coveney (UK e-Infrastructure Leadership Council and University College London) will present the “state of the nation” followed by a Provider’s Panel, Software, Training and User’s Panel – an important and timely opportunity for the community to review current progress and determine what’s needed in the future.

There’s a lot more happening throughout the event, including an exciting “DevChallenge” hackathon run by DevCSI, software surgery by the Software Sustainability Institute (SSI) and multiple community workshops – plus the Digital Research 2012 dinner in College and a reception in the spectacular Museum of Natural History in Oxford. Digital Research 2012 is very grateful to everyone who has come together to make this event possible, including e-Research South, Open Knowledge Foundation, Web Science, the Digital Social Research programme, our Digital Economy colleagues and the All Hands Foundation.

We look forward to seeing you at Digital Research 2012 in Oxford in September.

References

  1. Lazer, D., Pentland, A., Adamic, L., Aral, S., Barabasi, A.L., Brewer, D., Christakis, N., Contractor, N., Fowler, J., Gutmann, M. & (2009). Social Science: Computational Social Science, Science, 323 (5915) 723. DOI: 10.1126/science.1167742
  2. Stevan Harnad (2012). Open access: A green light for archiving, Nature, 487 (7407) 302. DOI: 10.1038/487302b

August 3, 2012

May 6, 2009

Michel Dumontier on Representing Biochemistry

Michel Dumontier by Tom HeathMichel Dumontier is visiting Manchester this week, he will be doing a seminar on Monday 11th of May,  here are some details for anyone who is interested in attending:

Title: Increasingly Accurate Representation of Biochemistry

Speaker: Michel Dumontier, dumontierlab.com

Time: 14.00, Monday 11th May 2009
Venue: Atlas 1, Kilburn Building, University of Manchester, number 39 on the Google Campus Map

Abstract: Biochemical ontologies aim to capture and represent biochemical entities and the relations that exist between them in an accurate manner. A fundamental starting point is biochemical identity, but our current approach for generating identifiers is haphazard and consequently integrating data is error-prone. I will discuss plausible structure-based strategies for biochemical identity whether it be at molecular level or some part thereof (e.g. residues, collection of residues, atoms, collection of atoms, functional groups) such that identifiers may be generated in an automatic and curator/database independent manner. With structure-based identifiers in hand, we will be in a position to more accurately capture context-specific biochemical knowledge, such as how a set of residues in a binding site are involved in a chemical reaction including the fact that a key nitrogen atom must first be de-protonated. Thus, our current representation of biochemical knowledge may improve such that manual and automatic methods of biocuration are substantially more accurate.

Update: Slides are now available via SlideShare.

[Creative Commons licensed picture of Michel in action at ISWC 2008 from Tom Heath]

References

  1. Michel Dumontier and Natalia Villanueva-Rosales (2009) Towards pharmacogenomics knowledge discovery with the semantic web Briefings in Bioinformatics DOI:10.1093/bib/bbn056
  2. Doug Howe et al (2008) Big data: The future of biocuration Nature 455, 47-50 doi:10.1038/455047a

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