Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
12 of 18 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary
Keywords from Contributors
Repository
IOTA: Integration Optimization, Triage and Analysis
Basic Info
Statistics
- Stars: 3
- Watchers: 12
- Forks: 4
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Deprecation notice: this is a deprecated repository. Please see the SSRL MC group software page and RnD for updated software lists and staff contact.
IOTA: Integration Optimization, Triage and Analysis
IOTA is a user-friendly front end for dials.stills_process, a serial
diffraction data processing program. IOTA is comprised of three main modules:
- Raw image import, pre-processing and triage
- Image indexing, lattice model refinement, and integration using
dials.stills_process - Analysis of the integrated dataset
IOTA can be run as a GUI or from the command-line; scripts can be used for both, interchangeably. The GUI has the advantage of displaying useful statistics; it can also be run in "monitor mode" during live data collection, during which the program will wait for new images to be written into the specified input folder. The command-line mode is useful if the program is run remotely on servers that do not, for some reason, support graphics.
Reference
Please note that IOTA is a front-end for other processing software. Therefore, the preferred construction for citation should be something like "data were processed with IOTA [1] using serial diffraction data reduction algorithms implemented in DIALS [2, 3]".
[1] IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT. J Appl Crystallogr. 2016 May 11;49(Pt 3):1057-1064
[2] DIALS: implementation and evaluation of a new integration package. Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K. & Evans, G. (2018). Acta Cryst. D74, 85-97.
[3] Improving signal strength in serial crystallography with DIALS geometry refinement. Brewster, A. S., Waterman, D. G., Parkhurst, J. M., Gildea, R. J., Young, I. D., O'Riordan, L. J., Yano, J., Winter, G., Evans, G. & Sauter, N. K. (2018). Acta Cryst. D74, 877-894.
For an example of how the IOTA/PRIME pipeline was used to solve a structure from a small dataset, see
[4] Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Elife. 2016 Oct 12;5.
Disclaimer Notice
The items furnished herewith were developed under the sponsorship of the U.S. Government (U.S.). Neither the U.S., nor the U.S. Department of Energy (D.O.E.), nor the Leland Stanford Junior University (Stanford University), nor their employees, makes any warranty, express or implied, or assumes any liability or responsibility for accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use will not infringe privately-owned rights. Mention of any product, its manufacturer, or suppliers shall not, nor is it intended to, imply approval, disapproval, or fitness for any particular use. The U.S. and Stanford University at all times retain the right to use and disseminate the furnished items for any purpose whatsoever. Notice 91 02 01
Work supported by the U.S. D.O.E under contract DE-AC03-76SF00515; and the National Institutes of Health, National Center for Research Resources, grant 2P41RR01209.
Owner
- Name: Macromolecular Crystallography at SSRL
- Login: ssrl-px
- Kind: organization
- Location: Stanford Synchrotron Radiation Lightsource
- Website: https://www-ssrl.slac.stanford.edu/smb-mc/content/documentation/manuals/software
- Repositories: 7
- Profile: https://github.com/ssrl-px
SSRL-PX operates and develops beamlines, providing state of the art facilities and support for visiting researchers.
GitHub Events
Total
- Push event: 1
- Fork event: 1
Last Year
- Push event: 1
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Artem Lyubimov | l****v@s****u | 228 |
| Artem Lyubimov | a****v | 118 |
| Markus Gerstel | m****l@d****k | 19 |
| Aaron S. Brewster | a****r@l****v | 10 |
| Oliver Zeldin | o****n@g****m | 9 |
| Nicholas Sauter | n****r@l****v | 7 |
| dermen | d****n@l****v | 5 |
| Nicholas Devenish | n****h@g****m | 3 |
| Nigel W Moriarty | n****y@l****v | 3 |
| Billy K. Poon | b****n@l****v | 3 |
| Monarin Uervirojnangkoorn | m****n@g****m | 3 |
| dwmoreau | d****u@l****v | 2 |
| Graeme Winter | g****r@g****m | 1 |
| Artem Lyubimov | a****t@d****u | 1 |
| James Parkhurst | j****t@d****k | 1 |
| terwill | t****r@n****g | 1 |
| Nigel W. Moriarty | N****y@L****v | 1 |
| Artem Lyubimov | a****t@a****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 6
- Average time to close issues: N/A
- Average time to close pull requests: 10 days
- Total issue authors: 0
- Total pull request authors: 4
- Average comments per issue: 0
- Average comments per pull request: 1.33
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- Anthchirp (3)
- ndevenish (1)
- dwmoreau (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 54 last-month
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Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 2
(may contain duplicates) - Total versions: 5
- Total maintainers: 3
pypi.org: iota
IOTA: Integration Optimization, Triage and Analysis
- Homepage: https://github.com/ssrl-px/iota
- Documentation: https://iota.readthedocs.io/
- License: BSD
-
Latest release: 1.5.4
published about 4 years ago
Rankings
conda-forge.org: iota
IOTA is a user-friendly front end for dials.stills_process, a serial diffraction data processing program.
- Homepage: https://github.com/ssrl-px/iota
- License: BSD-3-Clause
-
Latest release: 1.4.20
published almost 6 years ago
Rankings
Dependencies
- matplotlib *