Monday August 6th 2012
Realfagbygget (Science Building), Allégaten 41, University of Bergen, Bergen, Norway
This full-day Workshop is organised by the DDD Working Group (WG), appointed by the IUCr Executive Committee to define the need for and practicalities of routine deposition of primary experimental data in X-ray diffraction and related experiments. It will take the form of a one-day workshop to review progress during the Working Group's first year of activity.
Objective: To help frame a policy to be drafted by the IUCr DDD WG on raw diffraction data deposition for final approval by the IUCr Executive Committee.
There is a public forum for discussion of the issues covered in this workshop at http://forums.iucr.org
Timetable
9.00am Introduction and welcome. John Helliwell and Brian McMahon
9.05am The IUCr Diffraction Data Deposition Working Group Activities since IUCr Madrid
John R. Helliwella and Brian McMahon*b
aSchool of Chemistry, University of Manchester, M13 9PL, UK; bIUCr, 5 Abbey Square, Chester CH1 2HU, UK
[ Presentation (ppt, 1.4 MB)]
Abstract
It is increasingly important to deposit the raw data from scattering experiments; valuable information gets lost when only structure factors are deposited. Some research centres, e.g. synchrotron and neutron facilities, are fully aware of the need to archive raw data. Diamond Light Source, ISIS, the European PaN (Photon and Neutron facilities) and the Australian TARDIS initiatives are exemplars of good practice. Local university data repositories are also being developed, e.g. at the University of Manchester, relevant to laboratory X-ray diffraction data archiving. A globally registered digital identifier (such as DOI) for each significant dataset can therefore be obtained and linked to any related publication. A Working Group on the development of standards for the representation of data and associated metadata to permit the routine deposition of such raw data has been launched by the IUCr Executive Committee. Its title is 'Diffraction Data Deposition Working Group of the IUCr'. Its members include representatives from IUCr Commissions, synchrotron facilities, academic laboratories, structural databases, and inter-Scientific Union bodies on data and publications. There is a forum for 'Public input on diffraction data deposition' on the IUCr web site at http://forums.iucr.org, to which all interested parties are invited to contribute.
9.30am Motivations, challenges, horror stories and opportunities: Experiences of diffraction data management, archival and publication at the UK National Crystallography Service.
Abstract
The UK National Crystallography Service (NCS) provides data collection and full structural analysis services on small molecules and is a `Mid-range Facility' operating between the local research laboratory and the national synchrotron. The NCS has driven large-scale data management projects starting with CombeChem [1] and evolving to arrive at the Web2.0 world we work in today and the laboratory houses the most powerful laboratory-based small molecule diffractometer in the world. This level of service support has significant implications for the management, archival and publication of the diffraction data and structural results produced [2]:
1) Scale and volume (management): The NCS generates approximately an order of magnitude more data than the conventional research laboratory - this means that simply writing data to 'local' disks and labelling them has not been an option for many years. There is a difference in the approach to data management of diffraction images as opposed to derived and results data and as such we have adopted more conventional long-term storage options for these.
2) Scale and volume (dissemination): Generating so much data produces the follow-on issue of trying to publish and disseminate it. Derived and results data are stored and made available through information management, electronic laboratory notebook and repository systems - these are permanently available to authorised users, or in some cases openly online (http://ecrystals.chem.soton.ac.uk/). Managing raw data is rather more complicated and will be discussed in detail.
3) Accountability: As service providers we have a 'duty of care' for the diffraction data we collect on behalf of others - it is often many years before a collaborator comes back to the NCS and points out a problem with the analysis or wishes to publish the results. Moreover, as a large scale service operating in the modern age we are now moving into a policy-driven era of 'Service Level Agreements' and 'Terms and Conditions of Use', where we must commit to long term archival and curation of data on behalf of our users.
4) Disciplinary differences: As research becomes ever more inter- or multi-disciplinary, the systems we put in place for a particular discipline don't necessarily support the working practices and culture of others - the NCS laboratory now also houses instrumentation supporting macromolecular crystallography and materials science.
5) Institutional boundaries: The NCS provides data for researchers working in other institutions and operates out of both university and synchrotron facilities - this means data management crossing different technical, administrative and cultural boundaries.
[1] S.J. Coles, J.G. Frey, M.B. Hursthouse, M.E. Light, A.J. Milsted, L.A. Carr, D. DeRoure, C.J. Gutteridge, H.R. Mills, K.E. Meacham, M. Surridge, E. Lyon, R. Heery, M. Duke & M. Day, An E-Science Environment for Service Crystallography - from Submission to Dissemination, J. Chem. Inf. Model., (2006), 46, 1006-1016.
[2] S.J. Coles & P.A. Gale, Changing and challenging times for service crystallography, Chem Sci., (2012), 3, 683-689.
Simon J. Coles
UK National Crystallography Service, Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
[ Presentation (pptx, 40 MB)]
10.05am Report on several important EU projects: CRISP, PaNdata, NMI3, Biostruct X, HDRI and CALIPSO
Abstract
Recently, several EU FP7 programs have been started or are being started, which will have strong influence on IT user infrastructure at the European large facilities and the way experiments are performed at these facilities. They will affect a wide range of actions, such as user data policy, user identification, data continuum, to mention a few. In these programs, mainly facility people are involved. In order to be as efficient and useful as possible, however, information of and feedback from the facility users is essential.
Heinz J. Weyer
SwissFEL, Paul-Scherrer Institut, CH-5232 Villigen, PSI, Switzerland
[ Presentation (ppt, 1.6 MB)] [Supplementary presentation: Data Management Round Table ]
10.40am Linking raw experimental data with scientific workflow and software repository: some early experience in the PanData-ODI project
Abstract
Large facility providers often have developed mature data and publication infrastructure to capture the scientific outputs from experiments. The aim is not only to ensure the long term accessibility of these digital assets, but also demonstrate the prolonged impact of the research they support. Traditionally, the emphasis is on the cataloguing and archiving processes of the two ends: raw experimental data and publications. However, due to the rapidly rising data rate and volumes from scientific experiments and the complexity of certain types of data analysis, researchers become increasingly reliant on the infrastructure services provided by the facility operators.
This talk presents the early evidence we gathered in the PanData-ODI project in the data provenance work package to demonstrate the emerging needs in the community and to present some early snapshots of our approach to address the problem. In particular, we will examine the interplay of experimental data archive, scientific workflows and software repositories.
Erica Yang* and Brian Matthews
Scientific Computing, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Harwell, Oxford, Didcot OX11 0QX, UK
[ Presentation (pptx, 4.5 MB) | Presentation (pdf, 1.3 MB)]
11.15am Coffee break
11.35am Ten years and change: the MX data archive at ALS 8.3.1
Abstract
With very few exceptions, every image ever collected at the ALS beamline 8.3.1 since July 2001 has been backed up. So far, this is a little more than 4 million images and 66 terabytes on ~50,000 DVD-R disks, but more recently LTO4 tapes are being used as well so that second-copy failure modes are orthogonal to the first copy (~3000 images have proved unrecoverable). Assigning these ~20,000 datasets to PDB entries (~900 credited to 8.3.1) has proved difficult, as no metadata exists and nearly 700,000 images are called 'test'. Unit cell dimensions are not as unique in the PDB as one might expect, with one cell (48 62 84 90 101 104) within 5 Å and 5° of more than 1/5th of the entire PDB database! Exhaustive rigid-body refinement of all compatible-cell PDB entries against the 3000 MAD/SAD data sets collected between 6 and 11 years ago has revealed that ~50% of all unique crystal forms studied in that period have yet to appear in the PDB. Essentially all of these unpublished data sets are also unsolvable by application of modern MAD/SAD phasing techniques, but in one trial case from 2002, where the name of the protein was available, molecular replacement via the BALBES server proved successful. The original author is now working on the publication, but it is noteworthy that the search model that worked came from a structural genomics center in 2007, five years later. No doubt this is just one of many examples of structures that were not solvable with technology available at the time the data were collected, but remain scientifically valuable after sufficiently powerful methods are developed in the future.
James Holton
University of California, San Francisco and Lawrence Berkeley National Laboratory, USA
[ Presentation (ppt, 13.2 MB)]
12.10pm Continuous improvement of macromolecular crystal structures
Abstract
We propose that it is now feasible and desirable to develop mechanisms for continuous and systematic improvement of macromolecular crystal structures. It is feasible because of the availability of crystallographic data and the extensive automation of crystal structure determination and validation. It is desirable because small errors in interpretation can be fixed, improved methods for structure analysis can be applied, and groups of structures can be re-analyzed to extract maximal information about the set of structures. If raw diffraction data are deposited then the continuous improvement process can be more extensive than if only processed data are available, as raw diffraction data allows reprocessing of images, full confirmation of crystal symmetry, and even validation of the model using the original diffraction images. Key questions include how the various interpretations of a structure might be stored and how a user could find the most appropriate structure for their purposes.
Thomas C. Terwilliger
Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
[ Presentation (ppt, 0.1 MB)]
12.45pm Open Discussion
1.00pm Buffet lunch and soft drinks
2.00pm Towards policy for archiving raw data for macromolecular crystallography: Recent experience
Abstract
The need to consider what constitutes exemplar levels of metadata and raw diffraction data deposition, including the possibility of lossless compression, to be associated with future macromolecular crystallography publications is a pressing need. We have recently undertaken a relevant practical examination of procedures to liaise between distant research centres, Utrecht and Manchester, for network transfer of diffraction data images within a real research study (two anti-cancer drugs binding to a test protein, lysozyme). The prospects for local University archiving are being explored within a Research Data Management Service (RDMS) for the University of Manchester. Data of eleven lysozyme crystals, co-crystallized with cisplatin, carboplatin, DMSO and NAG (N-acetylglucosamine), were measured using two diffractometers and processed with four software packages [1]. Most of the crystals diffracted to 1.7 A. In total the data take 35.3Gb of disk space, and 20Gb when compressed (using the LZW algorithm of ncompress for lossless data compression). The diffractometers were equipped with completely different detectors: an R-axis IV imaging plate (with 3000x3000 pixels and 300mm diameter) and a Bruker Platium135 CCD (with 1024x1024 binned pixels and 92x92 mm2). Measurement strategies are determined by the detector aperture (size and distance) and the design of the goniometer. Based on 4/mmm point group symmetry the average redundancy of the Rigaku and Bruker data was 21.1 and 22.4 respectively, which corresponds to 4.5 and 12.0 per Gb. The equipment's data collection software writes vital information about the experimental set-up in the header of the images, such as the detector type, pixel size, overflow handling, the wavelength (trivial in case of a home source), the sample-to-detector distance, the goniometer axes and detector swing angle, the rotation axis and range, hopefully sufficient for any alien data processing software to correctly interpret the data. The images were processed by the internal software of the equipment, either d*Trek or Proteum2, and with Mosflm [2] and EVAL [3]. The EVAL software suite can read compressed images, so all EVAL data processing was done with compressed raw data. A comparison of the data processing and refinement statistics is made. Problems that were encountered will be discussed. They relate to distortion and flood field corrections, the necessity to refine cell orientation matrices, the establishment of crystal slippage and loss of tetragonal symmetry and removal of reflections affected by diffraction of ice. The paper describing this analysis [4] will make reference to the raw data archived at the University of Manchester, and each data set will have an associated DOI and reference to RCSB.
[1] Tanley, S.W.M, Schreurs, A.M.M., Kroon-Batenburg, L.M.J., Meredith, J., Prendergast, R.,Walsh, D., Bryant, P. , Levy. C. & Helliwell, J.R. (2012), Acta Cryst. D68, 601-612.
[2] Leslie, A.G.W. & Powell, H.R (2007). Evolving Methods for Macromolecular Crystallography. 245 41-51, ISBN 978-1-4020-6314-5
[3] Schreurs, A.M.M., Xian, X. & Kroon-Batenburg, L.M.J. (2009). Journal of Applied Crystallography 43, 70-82
[4] Tanley, S.W.M, Schreurs, A.M.M, Helliwell, J.R. & Kroon-Batenburg, L.M.J. (2012), J. Appl. Cryst. Submitted.
Loes M. J. Kroon-Batenburg*a, Antoine M. M. Schreursa, Simon W. M. Tanleyb and John R. Helliwellb
aCrystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; bSchool of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9PL, UK
[ Presentation (pptx, 1.3 MB)]
2.35 pm Some Economic Considerations for Managing a Centralized Archive of Raw Diffraction Data
Abstract
An analysis is presented of the costs associated with the data capture; annotation and validation; delivery and archiving for raw diffraction data. The scientific and technical staffing requirements as well as the requisite IT infrastructure resources are included in this analysis. A number of alternative archiving and delivery technologies are described providing a range of data availability, performance, and fault-tolerance. The costs of managing a large data collection of this type using local infrastructure are compared with the costs of a cloud-based solution.
RCSB PDB is supported by NSF, NIGMS, DOE, NLM, NCI, NINDS and NIDDK.
John Westbrook
RCSB PDB, Rutgers University, Piscataway, NJ, USA. E-mail: [email protected]
[ Presentation (ppt, 18 MB) | Presentation (pdf, 21 MB)]
3.10pm A vision involving raw data archiving via local archives as a supplement to the existing processed data archives (PDB, CSD, ICDD etc)
Abstract
The International Union of Crystallography (IUCr) is investigating the advantages for the crystallographic community of requiring, rather than only encouraging, the archiving of raw, unprocessed, experimental data - typically in the form of diffraction images - measured from a crystal, a fibre or a solution. The issue is being evaluated by an IUCr Working Group (see http://forums.iucr.org/). Such archiving could allow as yet undeveloped processing methods to have access to the originally measured data; and archiving raw data could help to reduce the occurrence of scientific fraud.
On the other hand, raw data sets are orders of magnitudes larger than structure factors and molecular coordinates. The debate within our community about this much larger proposed archiving effort revolves around the issue of 'cost versus benefit'. Costs can be reduced by preserving the raw data in local repositories, either at centralized synchrotron and neutron research institutes, or at research universities.
In parallel developments, sensitivities to avoiding research malpractice are encouraging Universities to establish their own data repositories for research and academic staff. These various 'raw data archives' would complement the existing processed data collections available through the curated structural databases and IUCr journals.
They would, however, most likely have gaps in their global coverage arising from the variability in the level of resources that individual institutions would be able to provide. In some cases, there are initiatives to provide centralized resources to multiple institutions (for example, the TARDIS project [1] provides federated indexing and discovery services for Australian universities). Assignment of unique identifiers by central authorities such as DataCite [2] will also help to assemble in a uniform format the metadata required to allow the creation of global federated services for the management and interrogation of archives of raw data sets.
We therefore believe that a realistic vision for the future includes a sufficiently large raw data archive, with reasonable global coverage, achieved through distributed and federated repository services.
[1] Androulakis, S., J. Schmidberger, Bate, M. A., DeGori, R., Beitz, A., Keong, C., Cameron, B., McGowan, S., Porter, C. J., Harrison, A., Hunter, J., Martin, J. L., Kobe, B., Dobson, R. C. J., Parker, M. W., Whisstock, J. C., Gray, J., Treloar, A., Groenewegen, D., Dickson, N. & Buckle, A. M. (2008). Federated repositories of X-ray diffraction images. Acta Cryst. D64, 810-814 [ doi:10.1107/S0907444908015540 ]
[2] DataCite (2009). http://www.datacite.org
John R. Helliwell*a, Brian McMahon*b and Thomas C. Terwilligerc
aSchool of Chemistry, University of Manchester, M13 9PL, UK; bIUCr, 5 Abbey Square, Chester CH1 2HU, UK; cLos Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
[ Presentation (ppt, 0.63 MB)]
3.45pm Invite remote participants to make comments and open discussion [There may be Workshop participants connecting via remote access, probably Skype.]
4.20pm Summing up. John R. Helliwell and Brian McMahon
4.30pm Close of Workshop
6.00pm ECM27 Opening Ceremony