ISPyB
Original author(s) European Synchrotron Radiation Facility (ESRF) and E-Science Resource for High Throughput Protein Crystallography (e-HTPX)[1]
Developer(s) ISPyB Collaborative Group[1]
Initial release June 30, 2017 (2017-06-30)[2]
Stable release

 (January 11, 2021; 3 years ago (2021-01-11))

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Written in Java, JavaScript[3]
Operating system Cross-platform
Type Laboratory informatics software
License(s) GNU Lesser General Public License v3.0[4]
Website ispyb.github.io/ISPyB
www.esrf.fr/ispyb

ISPyB (Information System for Protein Crystallography Beamlines) is a free open-source laboratory information management system (LIMS) for protein crystallography experiments on synchrotron beamlines, released under the GNU Lesser General Public License v3.0.

Product history

With the age of high-throughput crystallography (HTX) being ushered in at the turn of the century, an increased need for improved data management of experiments conducted at synchrotron-based HTX faclities was required. In 2001, a prototype LIMS named PXWeb was developed byt the European Synchrotron Radiation Facility (ESRF) for HTX experiments, but it quickly proved insufficient for the needs of ESRF. In conjunction with the E-Science Resource for High Throughput Protein Crystallography (e-HTPX) project, ESRF began work in 2003 to "reassess both the use cases deployed and the technology upon which PXWeb was based."[5] The end result in 2005 was ISPyB (Information System for Protein Crystallography Beamlines), a LIMS that "provided more sophisticated sample tracking and experiment recording features and facilitated the transmission of information from/to other LIMS."[5][6] By 2011, the likes of Diamond Light Source (DLS) were directly involved with the private development of ISPyB.[5]

By June 2015, ISPyB appeared on GitHub.[7]

In January 2017, a memorandum of understanding was signed by ESRF and a number of other European research institutions to further collaboratively develop ISPyB.[1][8] By June 2017, an initial 5.0.0 release of ISPyB appeared on GitHub.[2] As of October 2023, the latest version of ISPyB is 5.28, released January 11, 2021.[3]

Features

A full explanation of features is elusive, but Diamond has this to say[9]:

  • Create sample shipments and track them to the beamline
  • Manage sample, crystal and protein information
  • Monitor in real-time your data collections
  • View historical experiment and data analysis information
  • Create and edit experiment reports
  • Export your experiment's meta-data back to your home lab

Hardware/software requirements

MySQL is required, at a minimum, but a full list of installation requirements isn't given. Installation instructions can be found on GitHub.

Videos, screenshots, and other media

Entities using ISPyB

Entities known to be using ISPyB include[1]:

ALBA Synchrotron, Diamond Light Source (DLS), European Molecular Biology Laboratory (EMBL), European Synchrotron Radiation Facility (ESRF), Global Phasing Ltd., Helmholtz-Zentrum Berlin (HZB), MAX IV Laboratory, SOLEIL

Further reading

External links

References

  1. ↑ 1.0 1.1 1.2 1.3 ISPyB Collaborative Group. "ISPyB". GitHub. https://ispyb.github.io/ISPyB/. Retrieved 27 October 2023. 
  2. ↑ 2.0 2.1 "ISPyB v5.0.0". GitHub, Inc. 30 June 2017. https://github.com/ispyb/ISPyB/releases/tag/5.0.0. Retrieved 27 October 2023. 
  3. ↑ 3.0 3.1 ISPyB Collaborative Group. "ispyb / ISPyB". GitHub. https://github.com/ispyb/ISPyB. Retrieved 27 October 2023. 
  4. ↑ "ISPyB / LICENSE". GitHub, Inc. https://github.com/ispyb/ISPyB/tree/master/licence. Retrieved 27 October 2023. 
  5. ↑ 5.0 5.1 5.2 Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W.; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J. et al. (15 November 2011). "ISPyB: an information management system for synchrotron macromolecular crystallography" (in en). Bioinformatics 27 (22): 3186–3192. doi:10.1093/bioinformatics/btr535. ISSN 1367-4811. https://academic.oup.com/bioinformatics/article/27/22/3186/195018. 
  6. ↑ Beteva, A.; Cipriani, F.; Cusack, S.; Delageniere, S.; Gabadinho, J.; Gordon, E. J.; Guijarro, M.; Hall, D. R. et al. (1 October 2006). "High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline". Acta Crystallographica Section D Biological Crystallography 62 (10): 1162–1169. doi:10.1107/S0907444906032859. ISSN 0907-4449. https://scripts.iucr.org/cgi-bin/paper?S0907444906032859. 
  7. ↑ delageniere (8 June 2015). "Initial commit". https://github.com/ispyb/ISPyB/commit/550f418d842fe9c315aafbdf5f2f1fe539b40e8e. Retrieved 27 October 2023. 
  8. ↑ "ISPyB". European Synchrotron Radiation Facility. https://www.esrf.fr/ispyb. Retrieved 27 October 2023. 
  9. ↑ "ISPyB/SynchWeb". Diamond Light Source. https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Using-ISPyB.html. Retrieved 27 October 2023. 
source: https://www.limswiki.org/index.php/ISPyB