Difference between revisions of "ISPyB"
From LIMSWiki
Jump to navigationJump to searchShawndouglas (talk | contribs) (Created stub. Saving and adding more.) |
Shawndouglas (talk | contribs) (Finished adding rest of content.) |
||
| Line 25: | Line 25: | ||
==Product history== | ==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."<ref name="DelaganiereISPB11">{{Cite journal |last=Delagenière |first=Solange |last2=Brenchereau |first2=Patrice |last3=Launer |first3=Ludovic |last4=Ashton |first4=Alun W. |last5=Leal |first5=Ricardo |last6=Veyrier |first6=Stéphanie |last7=Gabadinho |first7=José |last8=Gordon |first8=Elspeth J. |last9=Jones |first9=Samuel D. |last10=Levik |first10=Karl Erik |last11=McSweeney |first11=Seán M. |date=2011-11-15 |title=ISPyB: an information management system for synchrotron macromolecular crystallography |url=https://academic.oup.com/bioinformatics/article/27/22/3186/195018 |journal=Bioinformatics |language=en |volume=27 |issue=22 |pages=3186–3192 |doi=10.1093/bioinformatics/btr535 |issn=1367-4811}}</ref> 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."<ref name="DelaganiereISPB11" /><ref name="BetevaHigh06">{{Cite journal |last=Beteva |first=A. |last2=Cipriani |first2=F. |last3=Cusack |first3=S. |last4=Delageniere |first4=S. |last5=Gabadinho |first5=J. |last6=Gordon |first6=E. J. |last7=Guijarro |first7=M. |last8=Hall |first8=D. R. |last9=Larsen |first9=S. |last10=Launer |first10=L. |last11=Lavault |first11=C. B. |date=2006-10-01 |title=High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline |url=https://scripts.iucr.org/cgi-bin/paper?S0907444906032859 |journal=Acta Crystallographica Section D Biological Crystallography |volume=62 |issue=10 |pages=1162–1169 |doi=10.1107/S0907444906032859 |issn=0907-4449}}</ref> By 2011, the likes of Diamond Light Source (DLS) were directly involved with the private development of ISPyB.<ref name="DelaganiereISPB11" /> | |||
By June 2015, ISPyB appeared on GitHub.<ref name="ISPyBInitialGH">{{cite web |url=https://github.com/ispyb/ISPyB/commit/550f418d842fe9c315aafbdf5f2f1fe539b40e8e |title=Initial commit |author=delageniere |date=08 June 2015 |accessdate=27 October 2023}}</ref> | |||
In January 2017, a memorandum of understanding was signed by ESRF and a number of other European research institutions to further collaboratively develop ISPyB.<ref name="ISPyBGitHubStart" /><ref name="ESRFISPyB">{{cite web |url=https://www.esrf.fr/ispyb |title=ISPyB |publisher=European Synchrotron Radiation Facility |accessdate=27 October 2023}}</ref> By June 2017, an initial 5.0.0 release of ISPyB appeared on GitHub.<ref name="ISPyB5" /> As of October 2023, the latest version of ISPyB is 5.28, released January 11, 2021.<ref name="ISPyBGHCodeStart" /> | |||
==Features== | ==Features== | ||
A full explanation of features is elusive, but Diamond has this to say<ref name="DiamondISPyB">{{cite web |url=https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Using-ISPyB.html |title=ISPyB/SynchWeb |publisher=Diamond Light Source |accessdate=27 October 2023}}</ref>: | |||
* 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== | ==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 [https://github.com/ispyb/ISPyB GitHub]. | |||
==Videos, screenshots, and other media== | ==Videos, screenshots, and other media== | ||
==Entities using | |||
==Entities using ISPyB== | |||
Entities known to be using ISPyB include<ref name="ISPyBGitHubStart" />: | |||
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== | ==Further reading== | ||
* {{Cite journal |last=Beteva |first=A. |last2=Cipriani |first2=F. |last3=Cusack |first3=S. |last4=Delageniere |first4=S. |last5=Gabadinho |first5=J. |last6=Gordon |first6=E. J. |last7=Guijarro |first7=M. |last8=Hall |first8=D. R. |last9=Larsen |first9=S. |last10=Launer |first10=L. |last11=Lavault |first11=C. B. |date=2006-10-01 |title=High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline |url=https://scripts.iucr.org/cgi-bin/paper?S0907444906032859 |journal=Acta Crystallographica Section D Biological Crystallography |volume=62 |issue=10 |pages=1162–1169 |doi=10.1107/S0907444906032859 |issn=0907-4449}} | |||
* {{Cite journal |last=Delagenière |first=Solange |last2=Brenchereau |first2=Patrice |last3=Launer |first3=Ludovic |last4=Ashton |first4=Alun W. |last5=Leal |first5=Ricardo |last6=Veyrier |first6=Stéphanie |last7=Gabadinho |first7=José |last8=Gordon |first8=Elspeth J. |last9=Jones |first9=Samuel D. |last10=Levik |first10=Karl Erik |last11=McSweeney |first11=Seán M. |date=2011-11-15 |title=ISPyB: an information management system for synchrotron macromolecular crystallography |url=https://academic.oup.com/bioinformatics/article/27/22/3186/195018 |journal=Bioinformatics |language=en |volume=27 |issue=22 |pages=3186–3192 |doi=10.1093/bioinformatics/btr535 |issn=1367-4811}} | * {{Cite journal |last=Delagenière |first=Solange |last2=Brenchereau |first2=Patrice |last3=Launer |first3=Ludovic |last4=Ashton |first4=Alun W. |last5=Leal |first5=Ricardo |last6=Veyrier |first6=Stéphanie |last7=Gabadinho |first7=José |last8=Gordon |first8=Elspeth J. |last9=Jones |first9=Samuel D. |last10=Levik |first10=Karl Erik |last11=McSweeney |first11=Seán M. |date=2011-11-15 |title=ISPyB: an information management system for synchrotron macromolecular crystallography |url=https://academic.oup.com/bioinformatics/article/27/22/3186/195018 |journal=Bioinformatics |language=en |volume=27 |issue=22 |pages=3186–3192 |doi=10.1093/bioinformatics/btr535 |issn=1367-4811}} | ||
==External links== | ==External links== | ||
* [https://www.diamond.ac.uk/Instruments/Mx/Common/Common-Manual/Using-ISPyB.html ISPyB at Diamond Light Source] | |||
*[https:// | |||
==References== | ==References== | ||
Latest revision as of 18:34, 27 October 2023
| 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.
