Archive for the ‘Chemical IT’ Category

The challenges in curating research data: one case study.

Friday, April 28th, 2017
No Gravatar

Research data (and its management) is rapidly emerging as a focal point for the development of research dissemination practices. An important aspect of ensuring that such data remains fit for purpose is identifying what curation activities need to be associated with it. Here I revisit one particular case study associated with the molecular structure of a product identified from a photolysis reaction[1] and the curation of the crystallographic data associated with this study.

(more…)

References

  1. Y. Legrand, A. van der Lee, and M. Barboiu, "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix", Science, vol. 329, pp. 299-302, 2010. http://dx.doi.org/10.1126/science.1188002

Supporting information: chemical graveyard or invaluable resource for chemical structures.

Friday, March 31st, 2017
No Gravatar

Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[1] has an SI which is paginated at 907; almost a mini-database in its own right! Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]

(more…)

References

  1. J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. http://dx.doi.org/10.1021/jacs.6b13229
  2. M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, pp. 160018, 2016. http://dx.doi.org/10.1038/sdata.2016.18

The provenance of scientific data – establishing an audit trail.

Thursday, March 30th, 2017
No Gravatar

In an era when alternative facts and fake news afflict us, the provenance of scientific data becomes ever more important. Especially if that data is available as open access and exploitable by others for both valid scientific reasons but potentially also by those with other motives. Here I consider the audit trail that might serve to establish data provenance in one typical situation in chemistry, the acquisition of NMR instrumental data. 

(more…)

A nice example of open data (in London).

Sunday, March 5th, 2017
No Gravatar

Living in London, travelling using public transport is often the best way to get around. Before setting out on a journey one checks the status of the network. Doing so today I came across this page: our open data from Transport for London. 

(more…)

Open science and the chemistry lab of the future.

Thursday, February 9th, 2017
No Gravatar

The title refers to an upcoming symposium on the topic on 22-24 May, 2017.  I quote here some of the issues tabled for discussion:

(more…)

Revisiting (and maintaining) a twenty year old web page. Mauveine: The First Industrial Organic Fine-Chemical.

Thursday, February 2nd, 2017
No Gravatar

Almost exactly 20 years ago, I started what can be regarded as the precursor to this blog. As part of a celebration of this anniversary,[1] I revisited the page to see whether any of it had withstood the test of time. Here I recount what I discovered.

(more…)

References

  1. P.W. May, S.A. Cotton, K. Harrison, and H.S. Rzepa, "The ‘Molecule of the Month’ Website—An Extraordinary Chemistry Educational Resource Online for over 20 Years", Molecules, vol. 22, pp. 549, 2017. http://dx.doi.org/10.3390/molecules22040549

OpenCon (2016)

Friday, November 25th, 2016
No Gravatar

Another conference, a Cambridge satellite meeting of OpenCon, and I quote here its mission: “OpenCon is a platform for the next generation to learn about Open Access, Open Education, and Open Data, develop critical skills, and catalyze action toward a more open system of research and education” targeted at students and early career academic professionals. But they do allow a few “late career” professionals to attend as well!

(more…)

Pidapalooza!

Thursday, November 10th, 2016
No Gravatar

This is sent from the Pidapalooza event in Reykjavik, Iceland, and is a short collection of notable things I learnt or which attracted my attention.

(more…)

An inorganic double helix: SnIP.

Sunday, October 16th, 2016
No Gravatar
After sixty years of searching, the first non-templated double helical carbon-free inorganic molecular structure has been reported.[1] That is so neat that I thought to load the 3D coordinates here for you to interact with and then to explore the prospect of using these coordinates to add some value with e.g. some chiroptical calculations.

(more…)

References

  1. D. Pfister, K. Schäfer, C. Ott, B. Gerke, R. Pöttgen, O. Janka, M. Baumgartner, A. Efimova, A. Hohmann, P. Schmidt, S. Venkatachalam, L. van Wüllen, U. Schürmann, L. Kienle, V. Duppel, E. Parzinger, B. Miller, J. Becker, A. Holleitner, R. Weihrich, and T. Nilges, "Inorganic Double Helices in Semiconducting SnIP", Advanced Materials, vol. 28, pp. 9783-9791, 2016. http://dx.doi.org/10.1002/adma.201603135

Chemistry preprint servers (revisited).

Tuesday, August 16th, 2016
No Gravatar

This week the ACS announced its intention to establish a “ChemRxiv preprint server to promote early research sharing“. This was first tried quite a few years ago, following the example of especially the physicists. As I recollect the experiment lasted about a year, attracted few submissions and even fewer of high quality. Will the concept succeed this time, in particular as promoted by a commercial publisher rather than a community of scientists (as was the original physicists model)?

(more…)