Shawndouglas: Finished adding rest of content.

2023-10-27T18:34:52Z

Finished adding rest of content.

← Older revision		Revision as of 18:34, 27 October 2023
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==
	~~{{As of\|April 2018}}~~, ~~no public documentation exists for the software~~, ~~though the~~ installation requirements ~~are presumably similar to Bika LIMS~~.		[[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==
	~~A few screenshots can be seen on the [http://www.senaite.com/ main website].~~

	==Entities using ~~SENAITE~~==
			==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://~~github~~.~~com/senaite SENAITE] on GitHub~~
	*[https://community.~~senaite~~.~~org~~/ ~~Senaite discussion board]~~
	*[https://~~pypi.org~~/~~search~~/~~?q=senaite SENAITE~~] ~~on the Python Package Index (PyPI)~~

	==References==		==References==

Shawndouglas: Created stub. Saving and adding more.

2023-10-27T17:45:54Z

Created stub. Saving and adding more.

New page

{{Infobox software
| name = ISPyB
| title = ISPyB
| logo =
| screenshot = 
| caption =
| collapsible =
| author = European Synchrotron Radiation Facility (ESRF) and E-Science Resource for High Throughput Protein Crystallography (e-HTPX)<ref name="ISPyBGitHubStart">{{cite web |url=https://ispyb.github.io/ISPyB/ |title=ISPyB |work=GitHub |author=ISPyB Collaborative Group |accessdate=27 October 2023}}</ref>
| developer = ISPyB Collaborative Group<ref name="ISPyBGitHubStart" />
| released = {{Start date|2017|06|30}}<ref name="ISPyB5">{{cite web |url=https://github.com/ispyb/ISPyB/releases/tag/5.0.0 |title=ISPyB v5.0.0 |publisher=GitHub, Inc |date=30 June 2017 |accessdate=27 October 2023}}</ref>
| discontinued =
| frequently updated = yes
| programming language = Java, JavaScript<ref name="ISPyBGHCodeStart">{{cite web |url=https://github.com/ispyb/ISPyB |title=ispyb / ISPyB |work=GitHub |author=ISPyB Collaborative Group |accessdate=27 October 2023}}</ref>
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU Lesser General Public License v3.0<ref name="SENAITELicense">{{cite web |url=https://github.com/ispyb/ISPyB/tree/master/licence |title=ISPyB / LICENSE |publisher=GitHub, Inc |accessdate=27 October 2023}}</ref>
| website = [https://ispyb.github.io/ISPyB/ ispyb.github.io/ISPyB]<br />[https://www.esrf.fr/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==

==Features==

==Hardware/software requirements==
{{As of|April 2018}}, no public documentation exists for the software, though the installation requirements are presumably similar to Bika LIMS.

==Videos, screenshots, and other media==
A few screenshots can be seen on the [http://www.senaite.com/ main website].

==Entities using SENAITE==

==Further reading==
* {{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==

*[https://github.com/senaite SENAITE] on GitHub
*[https://community.senaite.org/ Senaite discussion board]
*[https://pypi.org/search/?q=senaite SENAITE] on the Python Package Index (PyPI)

==References==
<references />


[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]

ISPyB - Revision history

Shawndouglas: Finished adding rest of content.

Shawndouglas: Created stub. Saving and adding more.