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ImmuneSpace Service Interruption for Monday, November 12th
Ju Yeong Kim 2018-11-09

ImmuneSpace will be unavailable starting 12 pm PST Monday, November 12th, for a database server upgrade. The portal is expected to be back up by the end of the business day (4 pm PST).

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ImmuneSpace is looking for a great junior developer to join the team!
ehenrich 2018-10-12

We are excited to announce that we have an opening for a junior or early career software developer (0 - 2 years professional experience) on the ImmuneSpace team. Individuals with diverse backgrounds are strongly encouraged to apply. If you have any questions or want to learn more about the opportunity, please reach out to the current project manager, Evan Henrich, via immunespace@gmail.com.

You can learn more about the lab at https://research.fhcrc.org/gottardo/en.html.

Please apply at https://careers-fhcrc.icims.com/jobs/12305/software-development-engineer/job.

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ImmuneSpace Service Interruption for Wednesday, August 15th
Leo Dashevskiy 2018-08-08

ImmuneSpace will be unavailable starting 9 am PST Wednesday, August 15th, for an update to both the data and the server.
The portal is expected to be back up by the end of the business day (4 pm PST).

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New server and R API versions are now available.
Leo Dashevskiy 2018-05-07
We have upgraded our portal to be powered by the latest 18.1 version of LabKey (e.g. sharing of reports as well as editing them via the integrated RStudio Server is now available).

The ImmuneSpaceR package was also upgraded to version 1.7.3, which among other things brought the following improvements:
- the new R6 class system is now utilized
- new cleaner documentation is available here: http://rglab.org/ImmuneSpaceR/index.html
- raw gene expression matrices can now also be pulled via getGEMatrix()
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ImmuneSpace Service Interruption for Friday, January 26th
Leo Dashevskiy 2018-01-25
ImmuneSpace will be unavailable starting Friday 7 pm PST, January 26th, for fixes to address the Meltdown/Spectre bugs. The complete downtime is expected to be roughly a day and the server should be back up fully on Saturday afternoon, though, partial functionality (web interface and the the database, but not raw data or R analyses) could be available on Friday night.
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Software Upgrade Complete
ehenrich 2017-11-28
We completed our software upgrade yesterday. ImmuneSpace now has the latest versions of LabKey Server, ImmuneSpaceR, and our custom modules. Many of the changes were behind-the-scenes, but an important one is that now the modules and the API both use a dynamic query for Gene Expression data so any reports will be using the most recent data.
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ImmuneSpace Service Interruption for Monday, November 27th
Leo Dashevskiy 2017-11-22
ImmuneSpace will be unavailable starting 9 am PST Monday, November 27th, for an update to both the data and the server. The portal is expected to be back up by the end of the business day (4 pm PST).
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ImmuneSpace Service Interruption for Monday, October 2nd
Leo Dashevskiy 2017-09-26
ImmuneSpace will be unavailable starting 10 am PST Monday, October 2nd, for an upgrade.
The server is expected to be back up by the end of the business day (4 pm PST).
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ImmuneSpace Service Interruption for Monday, September 18th
Ju Yeong Kim 2017-09-12
ImmuneSpace will be unavailable starting 10 am PST Monday, September 18th, for an upgrade.
The server is expected to be back up by the end of the business day (4 pm PST).
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ImmuneSpace Service Interruption for Friday, July 28th
Ju Yeong Kim 2017-07-27
ImmuneSpace will be unavailable starting Friday 4 pm PST, July 28th, for capacity expansion work. The downtime is expected to be roughly a day and the server should be back up on Saturday afternoon (July 29th).
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ImmuneSpace Service Interruption for Friday, March 24th
Leo Dashevskiy 2017-03-23
ImmuneSpace will be unavailable starting Friday 10 am (Pacific time), March 24th, for an upgrade.
The downtime is expected to be roughly a day and the server should be back up in the evening.
This update will include the new LabKey server version (17.1), the new data release from ImmPort (DR20), numerous back-end changes and UI improvements.
We invite all users to take part in a new round of testing after the upgrade is completed.
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New data coming soon
Leo Dashevskiy 2017-03-15
We are actively working on making new data available as part of the ImmPort's latest data release (DR20). This new release included substantial schema changes, which required significant changes to our internal schema as well as to all of the associated tools. While our work is almost complete, we are still testing and validating these changes. New data is expected to be available by the end of the month.
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HIPC face-to-face meeting Mar 22-23 2017
Leo Dashevskiy 2017-03-15
We are pleased to participate in the next HIPC face-to-face meeting where we will unveil some new features we have been working on. For those of you not invited to this close meeting, don't worry, we expect some of these new features to be made public very soon. So stay tuned! Remember to follow the @ImmuneSpace Twitter handle for the latest news and updates.
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New data available
Raphael Gottardo 2016-07-27
We have recently loaded 2 new studies, part of ImmPort Data Release 19. These studies (and other recently updated studies) are highlighted on the home page, and can also be easily accessed by selecting the "Recently added studies" option in the Data Finder. Other updates part of ImmPort DR 19 were also propagated to the relevant datasets/studies. For more details please look at our release notes.
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New studies available
Renan Sauteraud 2016-04-27
We have recently loaded 10 new HIPC studies, part of ImmPort Data Release 18. These studies are highlighted on the home page, and can also be easily accessed by selecting the "Recently added studies" option in the Data Finder. Among other things, these studies include a large collection of flu transcriptomics data that can be used to perform meta-analyses. For more details please look at our release notes.
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Standardizing Flow Cytometry Immunophenotyping Analysis
Renan Sauteraud 2016-03-09
A new paper published in Scientific Reports by HIPC members and colleagues present the results of a coordinated analysis of samples across nine laboratories using standardized panels, reagents and operating procedures. Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. These algorithms were able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. All material including data, protocols and computer code can be downloaded from ImmuneSpace. In particular all automated analyses can be fully reproduced "live" using OpenCyto.
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ImmuneSpace public release
Raphael Gottardo 2016-01-15
We are pleased to announce that, today, ImmuneSpace became officially public. As part of this release, multiple datasets from human immune profiling studies are now publicly available. The ImmuneSpace platform offers users state-of-the-art computational tools to explore studies, integrate and analyze data across assays, and perform custom analyses. Additional HIPC datasets will be added on a rolling basis. Please follow @ImmuneSpace on Twitter for updates.
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ImmuneSigDB: A new compendium of immune signatures for GSEA
Raphael Gottardo 2016-01-13
As a result of a project supported by an Infrastructure and Opportunity Grant from the Human Immunology Project Consortium, Haining and colleagues have generated a collection of 5,000 annotated, immunology-specific gene sets and have used it to uncover shared and species-specific biology in mouse and human transcriptional responses to sepsis. The paper was published today in Immunity. This new collection of gene sets is available from MSigDB and can easily be used within ImmuneSpace using our built-in GSEA framework, simply select the "MSigDB c7" collection in the "Modules" dropdown menu. For more information on how to use our GSEA tool, please watch our tutorial.
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ImmuneSpace November update
Renan Sauteraud 2015-11-13
Our latest upgrades have brought the following improvements and new features to ImmuneSpace:
- A new automated registration system
- The new DataFinder replaces the study finder and allows to search for subset of participants matching selected criteria.
- Updated studies to ImmPort data release 15.
- New and updated tutorials and tours.
As well as back-end improvements to data management and performances.

Please try out these new features and report any bugs/issues using the support board.
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HIPC face-to-face meeting Nov 18-19 2015
Renan Sauteraud 2015-11-13
As usual, we will give a short update about the new data and features available in ImmuneSpace at the upcoming HIPC face-to-face meeting.
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ImmuneSpace Service Interruption for Thursday, October 22nd
Renan Sauteraud 2015-10-21
ImmuneSpace will be unavailable on Thursday morning (Pacific time), October 22nd, for upgrade. The downtime is expected to be roughly a day and the server should be back up in the evening. This update will include the new Data Finder, various back end changes and UI improvements.
We invite all users to take part in a new round of testing after the upgrade is completed.
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Redesigned support page
Raphael Gottardo 2015-04-24
The ImmuneSpace support page has been redesigned to feature a new issue tracker instead of the previous support board. Feel free to create a new issue if you encounter a bug/error or if you'd like to suggest a new feature. From now on, we will rely on the ImmuneSpace Google group for user based discussion or general questions and comments.
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Improvement and new features
Raphael Gottardo 2015-03-13
Our latest upgrade has brought the following improvements and new features to ImmuneSpace:
- Data updated to the latest ImmPort data release (version 12)
- The study finder has been updated with novel features:
   - Added Research Focus filters
   - Added HIPC watermarks on HIPC funded studies
   - Added the ability to filter recently uploaded/highlighted studies
- Re-organized flow datasets (FCS sample and control files are now separated)
- Added fcs_analyzed_results to the Data Explorer. You can now visualized flow cytometry data using the Data Explorer module.
- Fixed various user reported bugs/typos

Please try out these new features and report any bugs/issues using the support board. Enjoy!
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ImmuneSpace Service Interruption for Monday, March 9th
Renan Sauteraud 2015-03-05
ImmuneSpace will be unavailable on Monday morning (Pacific time), March 9th, for upgrade. The downtime is expected to be roughly half a day and the server should be back up early in the afternoon. This update will include many fixes and improvements that have been discussed in the previous weeks and bring us closer to a public release.
We invite all users to take part in a new round of testing after the upgrade is completed.
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Migration complete
Raphael Gottardo 2014-12-17
We are pleased to report that ImmuneSpace has been successfully migrated from the Fred Hutch to Amazon Web Services (AWS). The server is now in beta testing until the official public release. Please report any issues to the ImmuneSpace team via the support board.
Thank you!
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HIPC face-to-face meeting Nov 17-18 2014
Raphael Gottardo 2014-07-25
Please mark your calendar for the next HIPC meeting. As usual, we will give a short update about the new data and features available in ImmuneSpace.
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New R package for working with ImmuneSpace studies
Greg Finak 2014-06-16
We have a new (beta) release of the ImmuneSpaceR package, which facilitates accessing ImmuneSpace studies and data sets from within R.
If you are developing R-reports based on ImmuneSpace data, the package should simplify your task. It can be downloaded at http://www.github.com/RGLab/ImmuneSpaceR.
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