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[2] |
| Stable release |
5.28 (January 11, 2021) [±] |
| 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
- 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.
- 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.
External links
References
- ↑ 1.0 1.1 1.2 1.3 ISPyB Collaborative Group. "ISPyB". GitHub. https://ispyb.github.io/ISPyB/. Retrieved 27 October 2023.
- ↑ 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.
- ↑ 3.0 3.1 ISPyB Collaborative Group. "ispyb / ISPyB". GitHub. https://github.com/ispyb/ISPyB. Retrieved 27 October 2023.
- ↑ "ISPyB / LICENSE". GitHub, Inc. https://github.com/ispyb/ISPyB/tree/master/licence. Retrieved 27 October 2023.
- ↑ 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.
- ↑ 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.
- ↑ delageniere (8 June 2015). "Initial commit". https://github.com/ispyb/ISPyB/commit/550f418d842fe9c315aafbdf5f2f1fe539b40e8e. Retrieved 27 October 2023.
- ↑ "ISPyB". European Synchrotron Radiation Facility. https://www.esrf.fr/ispyb. Retrieved 27 October 2023.
- ↑ "ISPyB/SynchWeb". Diamond Light Source. https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Using-ISPyB.html. Retrieved 27 October 2023.
