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NOMAD

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NMR Online Management And Datastore. Presented at the Research Data Network workshop, St Andrews, 30 Nov 2016

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NOMAD

  1. 1. NOMAD NMR Online Management And Datastore JISC Research Data Network Day – St Andrews 30 November 2016
  2. 2. Nuclear Magnetic Resonance Spectroscopy Wikipedia • Most frequently, NMR spectroscopy is used by chemists and biochemists to investigate the properties of organic molecules. • Suitable samples range from small compounds analyzed with 1-dimensional proton or carbon-13 NMR spectroscopy to large proteins or nucleic acids using 3 or 4- dimensional techniques. • The impact of NMR spectroscopy on the sciences has been substantial because of the range of information and the diversity of samples, including solutions and solids. UK World Academia Total Academia Total 400 800 8-10 k 15-20 k How much does it cost to produce NMR data? Purchase of a NMR instrument - from £ 100,000 up to £ 1,000,000 or more (academic prices) Annual running cost (consumables + service) - starting at about £ 10,000 per year  ~50% could be using an automated workflow  Vendor split Bruker/(Varian)/Jeol – 70/20/10 How many NMR instruments is around the world?
  3. 3. Golden Age of NMR Spectroscopy Workflow sample ? Synthetic Lab NMR Lab NMR spectrum Productivity – 10 to 20 experiments per day
  4. 4. Golden Age of NMR Spectroscopy Workflow Synthetic Lab NMR Lab Data Storage Challenges & Problems • Where is my data? • What instrument should I use ? • How much machine time can I use ? • …
  5. 5. Online survey – Current NMR dataflow 26 12 9 9 9 0 5 10 15 20 25 30 SYNTHETIC CHEMISTRY STRUCTURAL BIOCHEMISTRY METABOLOMICS SOLID STATE OTHER Academia – 27 Responses 96 % 44 % 33 % 33 % 33 % Average NMR lab Number of instruments : 6 Number of sample changers : 4 Number of users : ~ 150 Number of experiments per month : ~ 4400 30 % 48 % 22 % Data volume per month Less than 20 GB 20 – 30 GB More than 30 GB (only 23 responses) What type of chemistry does your lab support ?
  6. 6. Online survey – Current NMR dataflow 5 18 10 2 0 2 4 6 8 10 12 14 16 18 20 OTHER CENTRAL FILE STORE LOCAL NAS OPTICAL OR USB 8 % 40 % 20 % 72 % Academia – 25 Responses Where do you archive NMR data in your lab? Academia – 27 Responses (87 %) Does your NMR data store provide a search facility? Yes. SQL database. Yes. Other. No 20% 76% 4% Industry – 4 Responses (13 %) 50% 50%
  7. 7. NOMAD – NMR Online Management And Datastore  Web based “cloud computing” system that provides a resilient searchable data-store and centralised control of automation for Bruker NMR instruments.  Current version 1.2 (prototype) – 6 Bruker instruments with sample changers, 260 research users, 350 users in teaching labs  Dataflow – 6 000 to 10 000 Experiments (20 -30 GB) per month - under construction 6
  8. 8. R-Search Experiment 1  Experiment 2  Experiment 3  Experiment 4  Experiment 5  Experiment 6  Experiment 7  Experiment X  … PURE-link (private) Compound 1  Compound 2  Open-Data (world readable) Additional Info • Molecular Structure • Verification • Multiplet reports • Versioning Project 1  Project 1 DOI-number PURE ELN DOI-number URL-Links Current Development – NOMAD 2.0 • Database functional without submission portal  easier distribution of the system, 1.2 and 2.0 can run parallel • Single point of access Changes in architecture PURE-link & Open Access NMR Data Repository
  9. 9. Open Access NMR Data Repository Why NMR spectroscopy does not have an equivalent of Protein Data Bank or Cambridge Crystallographic Data Centre? • NMR spectroscopy produces vast quantity of data with high proportion of waste. • There was no driving force for chemists to do an extra work. Current status – reprints of 1D spectra and multiplet/peak reports in published papers and S.I. 1H NMR (500 MHz, Chloroform-d) δ 6.97 (ddd, J = 8.1, 7.2, 1.7 Hz, 1H), 6.93 – 6.80 (m, 3H), 4.67 (s, 2H), 4.25 (q, J = 7.1 Hz, 2H), 3.87 (s, 3H), 3.82 (s, 0H), 1.75 (d, J = 2.7 Hz, 0H), 1.27 (t, J = 7.1 Hz, 3H). 1.27 (t, J = 7.1 Hz, 3H) ???
  10. 10. Open Access NMR Data Repository Could Open Access Data Policies could help with that? • For chemists, submitting of underpinning data is another extra chore that they are forced to do. • NMR data ends up in a file mixed wither other data identified by DOI  no possibility to search using molecular structure a spectrum features • NOMAD facilitates collection of NMR data together with various metadata and facilitates publication process required by Open Access Data policies. • Linking NOMAD instances together could create Open Access NMR Data Repository. Long term future vision NOMAD 1 Private cloud NOMAD 2 Private cloud NOMAD 3 Private cloud NOMAD Central Database Open Access Data Search • Structure • Spectrum Features

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