Date
2023-06-19
Heading
Urgent maintenance of SSBD OMERO
Content
Due to urgent maintenance of SSBD OMERO, there are problems viewing images. We are working to resolve the problem.
Date
2023-05-18
Heading
QTBD5Viewer - a visualizer for BD5-format files - is now available.
Content
QTBD5Viewer
https://github.com/openssbd/QTBD5Viewer - a visualizer for BD5-format files - is now available. It runs on Windows, macOS, and Ubuntu Linux. BD5-format is a unified file format for quantitative biodynamics data and SSBD:database provides various types of such data in BD5-format.
Date
2022-12-24
Heading
System maintenance, Jan 20, 17:00 - Jan 21, 17:00, 2023.
Content
Due to system maintenance, the SSBD database, SSBD repository, and related databases will be unavailable from January 20, 17:00, to January 21, 17:00. Sorry for the inconvenience.
Date
2022-11-30
Heading
System maintenance 9:00-17:00, Dec 7, 2022
Content
Due to system maintenance, SSBD might be unavailable between 9:00 am and 5:00 pm on Wednesday, December 7, 2022. Sorry for the inconvenience.
Date
2022-11-23
Heading
SSBD:database 2022.11 update
Content
We are pleased to announce the SSBD:database 2022.11 update, which includes 1123 image datasets (6.5TB).
Added datasets are 163-Wang-MitochondrialDyn, 186-Tsuboi-TumorDyn, 187-Tsuboi-TumorDyn, 197-Bannai-CalciumIonSignaling, 199-Ichimura-MulticellularDyn, 209-Kimura-SkinMorphology, 210-Takeo-HFregeneration, 218-Tanaka-CellSignallingDyn, 222-Dodo-RamanImaging, 224-Kamada-MitosisDyn, 225-Seiriki-WholeBrainDev, 226-Matsumura-WholeBrainDev, 227-Egoshi-RamanImaging, 228-Kanadome-CellInteration, 229-Yamada-GeneExpression, 233-Nishiyama-CellDyn, 234-Kobayashi-ChemotaxisDyn, 235-Hattori-SmartphoneBioImaging, 239-Miyamoto-MitochondrialDyn, 240-Yoshizawa-MitosisDyn, 241-Vu-TemperatureDyn, 242-Wazawa-CellDyn.
Date
2022-04-08
Heading
SSBD:database the second half of 2021 update
Content
We are pleased to announce the second half of the SSBD 2021 update in the cherry blossom season in Japan. The update includes 755 image datasets (569 GB) and one quantitative dataset (13MB).
The added datasets are 131-Wen-NeuronalNucDyn, 138-Ito-SPBDyn, 164-Ono-NeuPMCA, 170-Tsutsui-HookBM, 172-Yoshida-ERKTracheaDev, 177-Kinjo-cAMPsignalingDyn, 178-konagaya-CellMigration, 179-Kobachi-BLVRAactivity, 180-Watabe-Biosensoractivity, 183-Iwasaki-SpineDyn, 184-Tanaka-SpineDyn, 185-Hoshino-MyotubeCa2Signal, 188-Ipponjima-NHEKsCornification, 189-Kobayashi-NSCsDyn, 190-Iguchi-SpineDyn, 192-Hiroshima-SingleMolDyn, 194-Obashi-SpineDyn, 196-Sueda-GeneExpReg, 202-Miyagawa-ChemotaxisDyn, 203-Tanabe-SingleDyn, 205-Shen-CellPatterning, 206-Miyamoto-CiliaryMorphology, 207-Kuroda-FinMorphology, 211-Hiroshima-EGFRTracking, 212-Kajikawa-GeckoEmbryos, 213-Yoshida-SpindleDyn, 217-Sakai-iRFPactivity.
Date
2021-11-30
Heading
SSBD:database the first half of 2021 update
Content
We are pleased to announce the first half of the SSBD 2021 update, which includes 1799 image datasets (8TB) and four quantitative datasets (6MB). We have a plan for the second half of the 2021 update until next spring. Added datasets are 70-Yoshida-KTMTDyn, 72-Kyogoku-CytoplasmNucDyn, 120-Ding-CentromericDyn, 126-Imanishi-CellMorNuCyM, 127-Konishi-ERKDyn, 128-Muta-IECsERKDync, 129-Komatsu-ERKBiosensorActivity, 130-Sano-CellMigrationDyn, 161-Tanaka-MEFMitochondrial, 165-Kinjo-ERKactivity, 166-Takubo-ECsTrajectory, 171-Ochi-Hes1DynNPCs.
Date
2021-05-24
Heading
REMBI: Recommended Metadata for Biological Images
Content
Our TL Dr Onami joined discussions on metadata standards in biological image data sharing with an international bioimaging community lead by EMBL-EBI. They propose global metadata guidelines, REMBI: Recommended Metadata for Biological Images.
https://so.riken.jp/2021/05/24/rembi-recommended-metadata-for-biological-images/
Date
2021-05-11
Heading
[Press Release] Recommendations for global standards of open image data formats and repositories.
Content
TL Dr Shuichi Onami and Prof. Jason Swedlow (University of Dundee, UK) along with Global Bioimaging, an international consortium of the leading experts in bioimaging communities, released recommendations for bioimage data format standards and open access image data repositories. These recommendations contribute to accelerating the development of the bioimaging field through data sharing.
https://so.riken.jp/2021/05/11/sharing-global-standards-of-open-image-date/
Date
2021-04-28
Heading
Network maintenance on May 6
Content
Due to network maintenance, the SSBD:database, SSBD:repository, and the sister databases will not be accessible from 00:00 a.m. to 01:30 a.m. JST (GMT-9) on May 6 (Thu) 2021. Sorry for the inconvenience.
Date
2021-03-18
Heading
Network maintenance on Mar 23.
Content
Due to network maintenance, the SSBD:database/repository will not be accessible intermittently on Mar 23 afternoon. Sorry for the inconvenience.
Date
2021-02-25
Heading
Some BD5 APIs are not available
Content
Some BD5 APIs are not available now cause of the technical issue. We're working on a fix.
Date
2021-02-09
Heading
System maintenance on Feb 9
Content
Due to system maintenance, the 4D visualizer and APIs will not be available on Feb 9, 9:00-16:00. Sorry for the inconvenience.
Date
2021-01-16
Heading
System maintenance on 2021/1/22, 1/23
Content
Due to system maintenance, SSBD:database/repository will not be available from Jan 22 17:00 to Jan 23 17:00. Sorry for inconvenience.
Date
2020-12-24
Heading
SSBD 2020 Update
Content
SSBD 2020 update, the metadata database fully renewed, and 77 image datasets (7GB) and 4 quantitative datasets are added. We are plaining next database update in a half year for COVID-19 situation.
Date
2020-11-25
Heading
System maintenance
Content
We will be performing some maintenance work on the SSBD:database this week (2020-11-25). You may experience some service outage from time to time.
Date
2020-08-12
Heading
A new paper on BD5 is published in PLOS ONE
Content
A new paper "BD5: an open HDF5-based data format to represent quantitative biological dynamics data" is now published in PLOS ONE.
https://doi.org/10.1371/journal.pone.0237468
Date
2020-07-23
Heading
BD5 manual was updated.
Date
2020-04-28
Heading
A preprint paper on BD5 is available on bioarivx.
Content
A preprint paper on "BD5: an open HDF5-based data format to represent quantitative biological dynamics data" is available in bioarivx. doi:
https://doi.org/10.1101/2020.04.26.062976
Date
2020-02-07
Heading
REST API service is now returned to normal
Content
REST API service is now returned to normal operation.
Date
2020-02-03
Heading
SSBD:repository page is open + some minor updates
Content
We have opened SSBD:repository page. You can find it here
http://ssbd.qbic.riken.jp/repository.
We have made some minor updates to the system correcting some errors on past datasets and allowing more quantitative datasets to be accessed by REST API. We have also revised our Japanese page. For more details
http://ssbd.qbic.riken.jp/update
*Note: REST API is temporary unavailable (2020-02-03), we shall try to return it to service as soon as possible.
Date
2020-01-09
Heading
System maintenance notice (3 February 2020)
Content
The system will be under maintenance on 3 February 2019. SSBD database will not be available between 14:00~17:00 JST
Date
2019-11-20
Heading
2019 Release
Content
In 2019 there are now 687 BDML files which include 810,685,686 entries, and 4,162 image sets. Please visit the Resources page
http://ssbd.qbic.riken.jp/resources/ for more details.
Date
2019-11-15
Heading
System maintenance notice (20 November 2019)
Content
The system will be updated on 20 November 2019. SSBD database will not be available on that day.
Date
2019-09-12
Heading
Logo changed
Content
SSBD is now rebranded as SSBD:database with a new logo.
Date
2019-07-24
Heading
Latest update
Content
All the visualization data for quantitative data have been updated.
Error on Keller et al. 2010 had been reported and a new version of BDML/BD5 files have been updated.
Date
2019-07-22
Heading
System maintenance notice (24 July 2019)
Content
Due to system maintenance, SSBD database will not be available between. 14:00 - 17:00 on 24 July 2019,
Date
2019-01-04
Heading
System maintenance notice (Date: Jan. 25~28 (JST))
Content
Due to system maintenance, SSBD database will not be available between Jan. 25, 17:00 to Jan 28, 09:00 (JST)
Date
2018-11-15
Heading
2018 New Release
Content
453 sets of images and 103 sets of quantitative data were added. Please visit the Resources page
http://ssbd.qbic.riken.jp/resources/ for more details.
Date
2018-03-23
Heading
System maintenance - some disruption of service
Content
We are migrating to a new server. Some of the services are not available during this period. We hope to provide full service asap.
Date
2017-12-01
Heading
System maintenance notice (Date: Dec 4 JST)
Content
Due to system maintenance, SSBD database will be unavailable on Monday 4 December 2017
Date
2017-10-10
Heading
REST API v3 and manual have been released.
Content
A new REST API v3 has been released to support SSBD 3.0. Manual of the REST API has been updated.
Date
2017-10-03
Heading
BDML schema 3.0 and SSBD 3.0 released!
Content
BDML schema version 3.0, PDPML schema version 1.0, and OMICSBDML version 1.0 have been released. All BDML-files have been updated. 23 BDML-files and 280 image-sets have been added. SSBD database system was updated.
Date
2017-07-10
Heading
System maintenance notice (Date: July 10 (JST))
Content
SSBD will not be available on 10 July 2017 due to unscheduled maintenance
Date
2017-05-20
Heading
SSBD API notice
Content
SSBD REST API full service is now available.
Date
2017-03-01
Heading
SSBD API notice
Content
SSBD REST API coordsXYZ is currently unavailable due to recent system maintenance. The service will resume shortly. Please check back later.
Date
2017-02-19
Heading
System maintenance notice (Date: Feb. 20~ (JST))
Content
Due to system maintenance, SSBD database will be unavailable Feb. 20 to 28 (About 9 days, JST).
Date
2017-01-27
Heading
System maintenance notice (Date: Jan. 27~ (JST))
Content
Due to system maintenance, SSBD database will be unavailable Jan. 27, 5:00 pm to 28, 05:00 pm (About 1 day, JST).
Date
2016-11-25
Heading
New SSBD API
Content
SSBD REST API "coordinates" is now available to retrieve data for both BDML ver0.15 and 0.18 files. "coordsXYZ" API is also available for backward compatibility, but it will be phased out in the future.
Date
2016-10-04
Heading
137 BDML-files added
Content
14 BDML-files in C. elegans have been updated and 123 BDML-files in C. elegans, D. discoideum, PC-12 cell, and so on have been added.
Date
2016-10-04
Heading
SSBD API notice
Content
SSBD REST API coordsXYZ is currently under maintenance and is unavailable due to recent update. The service will resume shortly after the updates. Please check back later.
Date
2016-10-01
Heading
System maintenance notice (Date: Oct. 4 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Oct. 4, 2016 13:00 pm to 18:00 pm (About 5 hours, JST).
Date
2016-05-20
Heading
14 BDML-file added
Content
14 BDML-files and the corresponding microscopy images in C. elegans have been added.
Date
2016-04-11
Heading
OpenSSBD released and Web services updated
Content
OpenSSBD, an open-source version of SSBD, has been released. Viewer and RESTful API have been updated.
Date
2016-01-18
Heading
2 BDML-files added
Content
2 BDML-files in M. musculus and microscopy images in M. musculus, R. norvegicus, and D. discoideum have been added.
Date
2015-11-27
Heading
Phenochar and manuals updated!
Content
Phenochar has been updated (version 3 and 2 for BDML schema 0.15 and 0.18, respectively). Manuals about SSBD-RDF data have been added.
Date
2015-10-03
Heading
1 BDML-file added.
Content
1 BDML-file in D. discoideum has been added.
Date
2015-08-19
Heading
Viewer and RESTful API updated!
Content
Viewer and RESTful API have been updated.
Date
2015-03-19
Heading
System maintenance notice (Date: Mar. 19 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Mar. 19, 13:00 pm to 18:00 pm (About 5 hours, JST).
Date
2015-01-30
Heading
System maintenance notice (Date: Jan. 30 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Jan. 30, 09:00 pm to 31, 09:00 pm (About 1 day, JST).
Date
2014-11-20
Heading
BDML paper published online.
Date
2014-10-03
Heading
OmicsBDML schema 0.18 released! 20 files added.
Content
OmicsBDML schema version 0.18 have been released. 20 BDML-files in M. musculus and C. elegans have been added.
Date
2014-10-01
Heading
System maintenance notice (Date: Oct. 1 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Oct. 1, 2014 11:00 am to 12:00 am (About 1 hour, JST).
Date
2014-08-28
Heading
BDML schema 0.2 released!
Content
BDML schema version 0.2 has been released. All software have been updated.
Date
2014-06-18
Heading
BDML schema 0.18 released!
Content
BDML schema version 0.18 have been released. All BDML-files and software have been updated.
Date
2014-03-17
Heading
System maintenance notice (Date: Mar. 19 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Mar. 19, 2014 10:00 am to 13:00 pm (About 4 hours, JST).
Date
2014-03-07
Heading
System maintenance notice (Date: Mar. 8 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Mar. 8, 2014 09:00 am to 13:00 pm (About 4 hours, JST).
Date
2013-12-03
Heading
Visit us at MBSJ 2013 (booth: BioDB6)
Content
Visit us at MBSJ 2013 (booth: BioDB6)
Date
2013-12-02
Heading
94 BDML-files added.
Content
94 BDML-files in Zebrafish, and C. elegans have been added.
Date
2013-11-27
Heading
System maintenance notice (Date: Nov. 27 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Nov. 27, 2013 02:00 pm to 04:00 pm (About 2 hours, JST).
Date
2013-11-20
Heading
System maintenance notice (Date: Nov. 21 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Nov. 21, 2013 10:00 am to 01:00 pm (About 3 hours, JST).
Date
2013-11-11
Heading
System maintenance notice (Date: Nov. 12 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Nov. 12, 2013 04:00 pm to 07:00 pm (About 3 hours, JST).
Date
2013-10-03
Heading
17 BDML-files added.
Content
17 BDML-files in Zebrafish, D. melanogaster, and C. elegans have been added.
Date
2013-10-02
Heading
System maintenance notice (Date: Oct. 9 (JST))
Content
Due to system maintenance, SSBD database will be unavailable Oct. 9, 2013 10:00 am to 01:00 pm (About 3 hours, JST).
Date
2013-09-02
Heading
SSBD database and BDML schema released!
Content
SSBD database was opened. BDML schema version 0.15 and PDPML schema version 0.05 have been finalized and released.