Cytobank – As the cell flows

Releases

Release Notes for Cytobank 2.7
Published on: Apr 18, 2013 @ 17:10

We’ve incremented to the next sub version (2.7) with the release of our visual plate annotator interface, which allows users to lay out and annotate their plate-based experiments in a visual interface that mimics the actual plate used during sample acquisition. This manner of spatially arranging samples is aimed to facilitate high throughput annotation, and there are tools built in that are designed to facilitate annotating in patterns within and among plates. This functionality can be accessed through any of our premium functionality servers including DVS Cytobank and Enterprise Cytobank.

- Angela

Release Notes for Cytobank 2.6.2
Published on: Feb 22, 2013 @ 17:01

This release is largely comprised of functionality enhancements and stability improvements to SPADE, but also includes some features and fixes to general Cytobank functionality as well.

New Functionality

• Copy SPADE trees
• Download annotated SPADE trees
• Pop-out multiple biaxial plots from the SPADE tree viewer to view more than one 2D plot at once
• Select multiple bubbles
• Node size slider: adjust how node size is reflected visually
• Edit the name of Saved Illustrations
• Server admins are notified when MOTDs posted (maintenance messages)
• Helpful support materials added to green Getting Started box on Dose Response Analysis page (DVS and Enterprise Cytobank)
• Cleaned up and reorganized SPADE tree controls
• Hovering over a SPADE node now displays event count in addition to ID number
• Updated the upload applet
• Users can now only select one SPADE population (radio buttons instead of check boxes)
• Upload applet allows users to select files now (not just folders)
• Added a date “Updated” field for SPADE trees
• When public-access-only users make changes to a SPADE tree, they can click “Reset Visualization” and the tree will return to the last saved version
• Updated support text for the green Getting Started box within the SPADE tree viewer page
• Upgraded the download files client

Bug Fixes:

• Fixed the “Shared with me” Inbox filter on DVS Cytobank
• Changed “Target number of clusters” to “Target number of nodes” in SPADE setup
• Fixed an issue where users could end up with negative credits when cloning experiments
• Fixed a bug where tooltips (info buttons) were broken
• Fixed a bug where outer figure dimension labels were not appearing when an odd number of figure dimensions were enabled for standard plot views (non-heatmap, non-overlay)
• Fixed broken links in export success email
• Fixed a bug where removing a selected node from a bubble sometimes failed for SPADE trees
• Fixed a bug with selective clone that was bringing over more channels than indicated
• Stability improvements to SPADE
• Node selections persist when users flip through samples
• Layered SPADE bubbles are no longer hidden
• Blue-yellow color scale for SPADE tree now matches that in the Working Illustration
• Changing SPADE analysis name now updates the name in the header bar
• Select all nodes now populates the table of statistics
• Exporting SPADE bubbles to a new experiment now consumes 1 credit (Enterprise servers)

- Angela

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Release Notes for Cytobank 2.6-1-2
Published on: Jan 07, 2013 @ 19:54

New Functionality

• You can now generate and download annotated PDFs for SPADE analyses
• Performance upgrades for working with tailored gates
• Plot Statistics render more quickly

Bug Fixes:

• Tooltips were broken; now they are fixed (in other words, dwelling your cursor over the “i” on a frame header brings up a popup window with support information)
• All changes to SPADE settings trigger the save button.

- Jennifer and Angela

Release Notes for Cytobank 2.6, 2-6-0-2, 2-6-1, 2-6-1-1
Published on: Nov 02, 2012 @ 14:02

The big news from the release of our Cytobank 2-6 series is that SPADE is now available on our premium servers. Our developers have been hard at work enhancing the functionality over the past few months and we have been corresponding with early adopters to learn and implement their feedback. Dose Response Analysis is also now available on premium servers and will allow you to plot dose response curves and compute EC50 values for your titration data.

New Functionality

• SPADE is available on premium servers (Enterprise Cytobank and DVS Cytobank). Learn more here.
• Dose Response Analysis is available on premium servers
• Exports now happen in the background and a zip file is created and attached to the Experiment Details page
• Export and Import experiment variables allows you to upload/download a spreadsheet of your annotations to further automate the annotation process
• SPADE autosave happens more frequently
• SPADE analyses can now be renamed
• Alphanumeric sorting is now available in the dimension boxes
• We now have a note on IE that SPADE does not work on IE
• There is now a warning on Windows 7/IE9 that the gating applet does not work
• Compensation can now be used in SPADE analysis generation

Bug Fixes

• Other users in a shared experiment can see SPADE trees
• Fixes to accommodate long SPADE runs without marking them as defunct
• SPADE handles DiVa files
• Fixes to IE9 navigation
• Sharing an experiment now properly sends a notification email
• “Save and Return” goes to working illustration (cookies issue had redirection to Experiment Details page)
• Fixed link in export success email
• When “Show Gates” is active, the “Show Gates” statistic drop-down menu is now active (was temporarily broken)
• Some view-through plot bugs were fixed
• Pop-up support tips are not better formatted
• Default channel now selected for CyTOF files
• Removed presets functionality
• PDFs were not creating attachments
• Non-FCS files were not being added as attachments
• Attachments were not being cloned
• If the user collapsed the SPADE analysis setup content box (center pane) or the analysis controls content box (sidebar), they are now opened for a new analysis.
• There is now a button to go back to a SPADE analysis if you click on the static Population view from the SPADE analysis page
• The name of the saved SPADE analysis now shows up on the SPADE analysis page
• Merged nodes on SPADE analyses were jumping to upper left corner when samples were changed
• SPADE global coloring range was not using percentile clipping
• SPADE bubble labels stay put after a reload
• Import gates for tailored gates was misdefining populations
• Fixed reset visualization on SPADE analysis page
• SPADE analyses now show up on experiments that are viewed via projects
• SPADE now works on Windows 7/Chrome
• When a bubble was selected on a SPADE analysis, no other node information was showing up on the node attribute table
• Changing samples on SPADE analysis was resetting column selections on node attribute table to all channels
• 2-d plots on SPADE analysis page were not updating when samples were changed
• Cloning an experiment was obliterating the selection in FCS files dimension on the saved illustrations
• Selected bubbles were not showing up in the export box on SPADE analysis page
• SPADE copy analysis settings is fixed
• A user with public-only access to an experiment cannot create a SPADE analysis
• Global color setting on SPADE analysis now works when you change samples (was setting all nodes to black)
• Existing SPADE analyses are now visible to users with public-only access to an experiment
• A heatmap with an empty square now works (was throwing an exception)
• Changes to a SPADE analysis now register as a change to the whole experiment, updating the “Last updated” value
• Links in the “Did You Know?” frame now open in new tabs
• A user with project access to an experiment, where the project is set to view-only, no longer has access to the “reset working illustration” button
• Can no longer remove all the columns from the SPADE node attribute table
• The fold change baseline selected was not being saved for SPADE analysis setup
• Could not uncheck baselines on the SPADE analysis fold change setup page
• Inbox filters were temporarily broken
• Someone who uploads an experiment who has no other access to the experiment no longer sees it on the inbox

- Jennifer and Angela

Release Notes for Cytobank 2.5.6
Published on: May 25, 2012 @ 7:34

You may have noticed a few additional tweaks to PDFs pop up in the form of 2-5-5-1, -2, -3, and -4 releases over the past few weeks. Well, now that those adjustments have been made, we’ve rolled out our latest release of 2-5-6, including expanded FCS file support and admin tools. Read on to learn more about these as well as some bug fixes.

New Functionality

• FCS 3.1 files are now supported
• Administrators can now navigate back to the user database instead of having to return back to the Inbox

Release Notes for Cytobank 2.5.5
Published on: Apr 29, 2012 @ 17:54

We’ll be rolling out our next release tomorrow! Check out what we’ve been working on:

New Functionality

• In the Export Events box on the Working Illustration page, the name “Compensation” was changed to “Exported Compensation” to clear up possible confusion.
• The session timeout is set to 8 hours (increased from 3 hours) and a warning has been added to the green Getting Started box in the gating applet.
• There is a new filter in the Inbox called “My experiments and shared,” which displays your experiments plus ones shared with you (as per user request).
• If an Illustration is longer than 200 inches, an information message tells the user to open the resulting PDF with an alternate program such as Preview (for Macs) or with Adobe Illustrator (Mac or PC), as Adobe Reader cannot display a PDF exceeding these dimensions.

Release Notes for Cytobank 2.5.4
Published on: Mar 7, 2012 @ 17:13

Our latest release is live on our servers and features a number of functionality enhancement and some bug fixes.

New Functionality

• Users can now select size formats for their PDFs, including several fixed sizes (Letter, A4, and Poster) and two auto-fit sizes (Large and Infinite). This also resolves an issue where a lot of extra blank space was found at the end of PDFs. We’ll be publishing a blog post soon explaining all our recent PDF enhancements, so stay tuned.
• The FCS file list on the experiment summary page now loads independently from the rest of the page.
• Tailored gates can now be imported from an existing experiment.
• PDFs now display plots sized according to the specifications in the Working Illustration (64 px, 128 px, etc).
• Added a download progress bar to the Stanford FACS Facility import page.
• Added a session time-out reminder in the gating applet, informing people of the need to Save and Return if they plan to walk away from analysis for more than 8 hours.

Bug Fixes

• Fixed an issue with improper functioning of the name search fields (for setting PI/PR, sharing with someone, etc)
• The support page, which has been redesigned, now opens in a new browser tab.
• PDFs for saved illustrations no longer have a date/time stamp for the ‘Updated’ value in the header, since saved illustrations cannot be updated. Working illustrations still have that date/time stamp on the PDF.
• Blog links all open in a single tab, instead of spawning multiple tabs.
• For Stanford users, retrieving an experiment via a URL now uses one credit. (Credits may be increased any time.)
• Compensation files are no longer shown as options for the “Percent in Gates” selected gate drop-down.
• When an experiment is cloned, its associated labels are no longer cloned.
• X axis labels had disappeared from plots shown on the upload success page; they are restored.
• An issue was occurring where a gate was set to tailored gate status, check gates was clicked, and then additional gates were tailored, and a subsequent “Check Gates” did not reflect the newer gate positions. This is now fixed.
• Fixed an issue where users were not warned when they had “Use Channel/Panel Values” selected but did not have the Channels figure dimension enabled. This was previously causing an error.
• Resolved an issue resulting in truncation of plots horizontally in PDFs when long row labels were present.

- Jennifer and Angela

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Release Notes for Cytobank 2.5.3.4
Published on: Feb 13, 2012 @ 15:36

We just released a fix for the Yahoo OpenID login button, which was briefly not working following an update by Yahoo.

- Angela

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Release Notes for Cytobank 2.5.3.3
Published on: Feb 7, 2012 @ 18:31

Today we released an update that fixes a bug that was causing some users to be unable to select their name as PI, PR, or in the sharing box.

- Angela

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Release Notes for Cytobank 2.5.3.2
Published on: Jan 21, 2012 @ 13:22

We released a quick update that directs users to our newly redesigned Support page when they click the “Support” link at the top of the Cytobank page.

- Angela

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Release Notes for Cytobank 2.5.3
Published on: Jan 11, 2012 @ 18:32

This round, we’ve added new functionality to help guide your user experience along more smoothly. We’ve added more instructions and messages to guide you along the way, as well as some other functionality and bug fixes. As always, let us know what you’d like to see happen next!

New Functionality

• A user’s PI (designated by the user) is now given full access to the user’s experiments by default. Access can be removed by
  unchecking the checkbox when creating the experiment or by removing the user on the experiment summary page.
• The ability to assign kits to experiments has been removed.
• If there are channel conflicts, a warning message is displayed on the main illustration page.
• The clearer description of permissions levels is provided when setting up projects.
• The import file compensation page has clearer instructions.

Bug Fixes

• Long column names now wrap properly in PDFs
• Improved the performance of opening illustrations for experiments with many tailored gates
• Improved the performance of running the “Check gates” functionality when using tailored gates on a large number of files
• Fixed a bug with quad, split, and range gates
• Exports made with the “FCS Files” dimension active no longer have “.fcs” in the middle of the filename
• The “Top Channels” Inbox filter is working again
• Colors can now be selected for contour and shaded contour plots
• Attachments now properly show who uploaded them (previously, they showed the experiment owner as the uploader)

- Angela and Jennifer

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Release Notes for Cytobank 2.5.2
Published on: Nov 30, 2011 @ 17:54

The newest release of Cytobank has incorporated a hodgepodge of useful functionality and bug fixes to improve your user experience. Check out what’s new!

New Functionality

• There is a status page for Cytobank employees to help us monitor performance and look for places to improve performance
• The default scaling parameters for CyTOF data files have been changed, as CyTOF software now spreads the data around zero. The new default parameters are the following: Scale = Arcsinh, Cofactor = 5, Min = -5, Max = 12,000
• Graphics tweak: the shadow for tooltip popups is now black instead of gray; this will make the look of plots behind the tooltip a little cleaner
• If a user selects only one channel when creating a compensation matrix, an error message now appears asking the user to select at least two channels, and channel options are presented again
• Reworded “Request more credits” to “Get more credits” to reflect the fact that credits are always immediately available upon request

Bug Fixes

• Labels for the “overlaid” dimension on histogram overlays now appear on PDFs; they were missing from the new PDFs
• QR code has been fixed on the new PDFs for a minor URL problem
• Fixed a bug where clicking on a label to filter the inbox wasn’t working
• The sample name listed for the gating hierarchy on the new PDFs is now in original sample case instead of all caps
• Fixed a bug where labels for public experiments were not properly displayed on the experiment summary page
• If no populations are selected, you now get an error message when you try to export events reminding you to select a population

- Angela and Jennifer

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Release Notes for Cytobank 2.5.1
Published on: Nov 10, 2011 @ 14:55

The latest release of Cytobank is live on our servers, including some new functionality and a few bug fixes. Of note this time around, we’ve altered the way Inbox filters work. You can now filter the list of experiments you see in your Inbox by choosing to view only experiments you uploaded or those for which you are the primary researcher (“My Experiments”), experiments that others have shared with you directly or through projects of which you are a member (“Shared with me”), experiments that have been made public to everyone on Cytobank or your hosted server (“Public experiments”), experiments you have archived (“Archived experiments”), or experiments you have deleted (“Trash”). You can read more about the new experiment filters on our documentation site. Stay tuned for an upcoming post highlighting functionality that will help you keep your inbox organized!

New Functionality

•  The “Active experiments” inbox filter was renamed to “My experiments,” and now only displays experiments you uploaded or experiments for which you are the PR.
• The “Plate” figure dimension now pulls information from the PLATE_NAME attribute within FCS files, with PLATE_ID used in its absence.
• Added additional instructions to the autocompensation wizard pages.
• Added message notifying users when there are no experiment files present when a user attempts to display a gating hierarchy for all files (this feature will not work if only compensation files are present).

Bug Fixes

• The “Shared with me” filter now only shows experiments that were shared with you, either directly or via projects of which you are a member. We fixed a bug where experiments for which you were PR were showing up in this list if the experiments you owned were part of a project created by someone else that was shared with you (whew).
• Scale settings are now transferred when creating an experiment from gated files.
• Channel names for duplicated files now mirror that of the parent file when using the Duplicate Files feature on the annotation pages.
• Fixed a bug where a manager could not be added to a project.

- Angela and Jennifer

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Release Notes for 2.4.5.1 – 2.5.0.1
Published on: Nov 4, 2011 @ 9:45

In the latest releases to Cytobank, we have made some big improvements to PDFs of your saved illustrations. The biggest change you will notice is that the data contained in PDFs are now displayed on one continuous, scalable page. This makes it easier for you to excerpt your data when preparing figures, and fixes a previous issue with especially wide or long plot sets getting truncated. Stay tuned for a blog post that will put these changes in context.

Do you have any questions about the new functionality, or others? Email us at helpdesk@cytobank.org.

New Functionality

• PDFs now display all of the content on one scalable page
• You can now specify a name for PDFs prior to download
• The Gating Hierarchy display now mirrors that seen in the Working Illustration, using space more efficiently
• PDFs have a new look, with a cleaned-up header
• Added text instructing user how to figure out where the PDF was saved on their computer
• Added notification that PDF generation has completed
• When you download a PDF, it is automatically added to the experiment as an attachment, listed under Attachments on the Experiment Details page.

Bug Fixes

• Fixed an issue where gates and populations were migrating over to the new experiment when using Create Experiment from Gated Files

- Angela and Jennifer

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Release Notes for Cytobank 2.4.4 – 2.4.5
Published on: Sep 20, 2011 @ 17:20

The Cytobank developers have been busy bees, implementing features requested by our users and squashing new bugs as they arise. Of note, we have added a “selective cloning” feature that allows you to create a new experiment that contains a subset of an existing experiment’s FCS files. This would be a handy way to split files off into a new experiment if a subset of files use a different compensation matrix, or to separate debarcoded files generated with our “Create Experiment from Gated Files” feature (stay tuned for a post on Fluorescence Cell Barcoding).

As always, please email us at helpdesk@cytobank.org if you have any questions, want to report a bug, or would like to request a new feature. Read on for a summary of these changes.

New Features

• Selective cloning is now available. This allows a user to clone an experiment with a selection of FCS files (instead of all the files). Clone FCS files and Clone experiment (where all FCS files are used)
  are still available.
• There is a new “Profile” link at the top of the page to make it easier to get to your profile. Among the things you can do on your Profile page, you can change your email address, change your PI, and change the default contents of your Inbox when you first land on that page (e.g., to see only your experiments, or always see “All Experiments”). The “Welcome, Username” link will also bring you to your Profile page.
• A user’s PI is now the default PI on selective clones. All full access users are listed as options for PI. There is a checkbox to make it easy to give full access to the PI, similar to the one in place for creating new experiments.
• All attachments can now be downloaded in a single zip file.

Bug Fixes

• Fixed a bug where quad/split/range gates were not being drawn properly.
• When we updated projects so that managers have full access to all experiments regardless of the settings for members/leaders, there was a bug where existing managers already on a project were not getting access to the new experiments. Managers who were already on a project will have full access to experiments added to the project from now on. This is not retroactive for experiments that were on the projects before the last release.
• A bug was fixed that made “Percent in gate” unavailable as a plot statistic if “Ungated” was selected; now it’s only unavailable if no gates have been drawn
• The gating applet now handles large numbers of tailored gates without crashing.
• When gates are deleted, the status is saved in the gating applet (even without clicking “Save & Return”). This fixes a bug where deleting a gate and then importing gates led to the deleted gate sticking around.

- Jennifer and Angela

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Release Notes for Cytobank 2.4.3
Published on: Aug 8, 2011 @ 18:04

We recently rolled out our latest release to the servers. A couple changes we’d like to highlight. First, managers of projects now have full access to all experiments in those projects. (Read more about projects on our documentation site.) We’ll have a separate blog post discussing projects [updated 08/22/2011] and how you can use them to share groups of experiments with colleagues. Second, you can now archive experiments in your Inbox. This is a new feature that has been frequently requested, and we’re excited to finally roll it out to you to help you better organize your experiments!

Questions on these or other features? Email us at helpdesk@cytobank.org.

New Features

• Managers of projects now have full access to all experiments in those projects (regardless of the level of access set for project members). This is not retroactive for existing projects. Read more on our documentation site.
• You can now archive experiments in your Inbox. Archived experiments will be designated with an “A”. You will not see archived experiments unless you are viewing “All experiments” or “Archived experiments”. Read more about Inbox filters on our documentation site.
• We now handle FCS files exported from FlowJo that have blank reagent (long channel) names. This can result if you have not annotated the reagent (e.g. CD3 PE-A) in FlowJo. The field now defaults to the short channel name (e.g. PE-A).
• Creating an experiment from gated files (an option on the Working Illustration page) now works like a full experiment clone – all illustrations, annotations, and compensation files are included in the new experiment.
• Filenames ending in a letter and two numbers (e.g. filenameA01.fcs) are now recognized as plates. This is the default for files exported from CellQuest.

Bug Fixes

• Fixed an issue where a user’s PI/Manager could not be entered or updated on a user’s profile.
• Fixed an issue where kit-templated gates did not show up until you entered the gating applet.
• Clicking reset on an annotations page (such as Conditions or Timepoints) now prompts you to make sure you want to reset and remove all tags.

- Jennifer and Stephanie

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Release Notes for Cytobank 2.4.1.3 – 2.4.2
Published on: Jul 23, 2011 @ 12:32

We released a number of improvements and bug fixes to our servers over the past month. Most of these changes came about as a result of user questions or bug reports – please keep the great questions and feedback coming!

As always, please email us at helpdesk@cytobank.org if you have any questions, want to report a bug, or would like to request a new feature. Read on for a summary of these changes.

New Features

• Performance updates were made to speed up processing, particularly in experiments with a large number of compensated channels.
• You can now duplicate an FCS file in an experiment (instead of having to upload an additional copy of the file). This is useful in cases such as the following: 1) you want to assign a file to multiple conditions or doses or 2) you collect one unstained file but want to show it in an overlay for multiple staining panels.
• Tube name or sample name are now visible in addition to the filename in the drop-down menu in the gating applet. (Note that if the filename is too long, the tube or sample name may be either truncated or not displayed.)
• The experiment summary page now provides an estimate of an Illustration’s size and content by listing the Figure Dimensions used in the Illustration. Example: Channels (4) x Conditions (7) x Populations (1).

Bug Fixes

• If required information is not provided when creating an experiment, an error message is now generated.
• Fixed an issue with tailored gates being duplicated when copies of an existing file were added to the experiment.
• The percentile algorithm has been updated.
• Fixed an issue with the availability of the percent in gate statistic. The statistic is now available except in these instances:
  • When “Ungated” is selected, with or without other gates
  • When no gates are selected
• Fixed an issue with timestamps on Illustrations and experiments:
  • Saved illustrations now only display a “Created” timestamp.
  • The “Updated” timestamp for your Working Illustration is now updated when you click the “Update Illustration” button.
• Fixed an issue with experiments created from cloned files where a default channel was not selected (and thus a default illustration could not be displayed).
• Fixed an issue where Cytobank did not recognize “SS Log” as a side scatter channel.
• Renaming a tailored gate now renames the gate on all files.
• When importing compensation, gates, or annotations (such as conditions) from another experiment, the drop-down menu no longer lists the current experiment as the default.
• We have removed the Presets menu on the Working Illustration page (which set up Illustrations for specific pre-set conditions).

- Jennifer and Stephanie

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Release Notes for Cytobank 2.4.0.1 – 2.4.1.2
Published on: Jun 16, 2011 @ 11:00

We’ve released a considerable number of changes to Cytobank over the past six weeks. Many of these new features are not yet visible to our users, because they operate in the background to power Cytobank Reports. You can see Cytobank Reports in action by viewing the Report created for the Nolan Lab’s recent mass cytometry study. Cytobank Reports also powers the datasheets in the BD FACSelect Buffer Compatibility Resource. In the near future, users will be able to use these features and create their own Reports to showcase their data and analyses.

What is visible for our users is an updated interface for Figure Dimensions. We’re excited to introduce these changes, as we think they make selecting your files and rearranging plots even easier than before. We’ll be discussing these changes in more detail in a future blog post. [Updated 07/22/2011]

We’d love to hear your thoughts. Send comments and questions to helpdesk@cytobank.org.

New Features

• Functionality for Cytobank Reports has been added.
• The Figure Dimensions interface has been updated.
  • The “Edit” link on most Figure Dimensions is now called “Setup”.
  • A new link called “Choose” opens a lightbox (a pop-up window displaying the Dimension tags) where you can more easily select which tags you want to show in your Working Illustration.
  • You can now modify the layout of your plots by re-ordering the tags in the lightbox – drag them up and down using the gray “grab” handles. You can still re-order Dimension elements in the Layout Placeholders tab in your Working Illustration.
• You now have the option of selecting one or more cell types as “Source(s)” in your Experiment Details. You can also leave it blank.
• The list of files in the gating applet now displays more files per “page” in the drop-down menu.

Bug Fixes

• Improvements have been made to entering and exiting the gating applet.
• The compensation matrix in your Working Illustration is now set to what was last used in the gating applet.
• Import Gates (in the gating applet) now defaults to a blank selection, prompts for a confirmation to import gates from the selected experiment, and displays a success message.

- Jennifer and Stephanie

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Release Notes for Cytobank 2.3.4.1
Published on: Apr 29, 2011 @ 8:58

We rolled out Cytobank 2.3.4.1 on all of our servers this week. This update contains an important fix for those of you who have upgraded to Firefox 4, as well as layout changes to most of the Annotation pages.

The update this week fixes an issue with the gating applet that was preventing it from loading properly in Firefox 4. There are a few remaining issues that we are aware of. On a Mac, pop-up windows like “Manage Populations” do not seem to be working properly. Click on the Java icon that appears in the dock to see the pop-ups. If you get a Java icon in the gating applet area, try reloading your browser. As always, please submit a support ticket if you notice other issues.

Most of the Annotation pages have been updated for ease of use. The “Add” text box (in which you can type a comma-separated list of tags) has been moved to the main section of the page. These pages also now contain links to hop directly to the Timepoints, Dosages, Conditions, Individuals, or Sample Types pages. For example, after tagging your files with Timepoints variables, you can now click “Edit Conditions” under “Actions” on the left sidebar to be taken directly to the Conditions page, without having to return to your Working Illustration.

Do you have questions or comments about this new update? Please send us an email or submit a support ticket.

New Features

• The “Add” text box on most Annotation pages has been moved to the main section of the page.
• Links have been added to most Annotation pages to make it easy to hop to and between the Timepoints, Dosages, Conditions, Individuals, and Sample Types pages, without needing to return to the Working Illustration. Annotations are automatically saved as soon as you leave the Annotation page.
• “Getting Started” boxes have been added to most Annotation pages.

Bug Fixes

• The gating applet now loads properly in Firefox 4.
• Fixed an issue where turning a tailored gate back into a global gate deleted the associated population.

- Jennifer and Stephanie

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Release Notes for Cytobank 2.3.4
Published on: Apr 8, 2011 @ 18:00

We released Cytobank 2.3.4 to our production server this week, and we expect to release it on all of our hosted servers over the weekend. The most visible change to all users may be the new Getting Started boxes (more after the jump). Another change will be noticeable to those using Cytobank on their iPhone or iPad (see our recent blog post about Cytobank on the iPad).

The Getting Started boxes are the green boxes at the top of the Inbox, Experiment Details, Working Illustration, and Compensation pages, as well as at the top of the Gating Applet. (You may need to click on the arrowhead in the green title bar to expand these if you’ve previously minimized them.) We’ve updated the text and links in these boxes. The linked video tutorials open directly in a lightbox on the page so that you can view the video without losing your place in Cytobank. We hope these new Getting Started boxes will provide useful tips and guidance.

Please contact us via email, Facebook, or Twitter if you have comments or questions about the new Getting Started boxes or any of the other changes listed below.

New Features

• Gates are now drawn at one-pixel thickness regardless of plot size, for easier viewing.
• Export options for FCS files and gated events are now better organized on the Working Illustration page.
• You can now see the scale settings for someone else’s experiment if you have illustration access.
• The custom compensation matrix table now has more descriptive labels for the rows and columns.
• We’ve clarified that plot scales can be edited on your own experiment.
• Functionality on iOS devices (iPhone and iPad) is now improved for dragging and dropping (for example, rearranging Figure Dimension boxes).
• A link to our blog has been added to the top of the Cytobank application.
• “Delete My Saved Illustrations” now provides a warning popup to fend off accidental clicks.
• Emails that notify users about experiments that have been shared with them now reply to the experimenter’s email address (instead of a generic Cytobank support address).
• Pairwise plots (accessible from “Advanced Views” on the Working Illustration) now have tooltips, popups that appear when you hover over the plot that provide the X and Y axis labels, to help identify plots in matrices that are very large.
• Getting Started boxes have been updated with new text and tutorial videos that open up in a lightbox on the current page.

- Jennifer and Stephanie

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Release Notes for Cytobank 2.3.2 – 2.3.3
Published on: Mar 21, 2011 @ 15:36

Over the past month, we’ve continued adding new features and fixing identified bugs. Below is a summary of the most visible changes.

One change that may not be immediately apparent to existing Cytobank users is that we now send an email verification link to new users when they first register. We also send a verification link if existing users update their email addresses. Users will still be able to access Cytobank if they haven’t yet verified their (new) email address.

Need to update your registered email address? Click “Profile” at the top of the Cytobank application and then click “Edit” in the left sidebar.

Questions or comments? Please get in touch with us by sending us an email or clicking “Feedback” in the footer of the application. We’d love to hear from you!

New Features

• Functionality for pairwise plots is now available under “Advanced Views”
• A new “Delete My Saved Illustrations” button on the Experiment Details page enables users to delete all of their saved illustrations for that experiment
• “Help” link has been renamed “Support”
• Tube name is now extracted from DiVa files in various places such as compensation pull-down menus
• The success page for file upload now includes file size units
• New statistic has been added: Pearson R (X vs Y), which reports the correlation coefficient for the x-axis vs the y-axis (note that this is not available for histograms, heatmaps, or heat plots)
• Top Channels now loads only when requested, enabling the Inbox to load more quickly
• The option to export a table of scaled events is now available
• We now verify email addresses when users first register and if/when they update their email addresses
• Scales for Accuri experiments are now set automatically (similar to CyTOF)

Bug Fixes

• Experiments can now be permanently deleted from Trash
• Fixed an issue where plot statistics could not be turned off for heatmaps and heat plots
• Fixed an issue where exported Table of Events only contained the first row of values repeated if compensation was enabled
• Fixed a rare issue where the cache reads a file incorrectly
• Fixed an issue where some support tickets were not being sent correctly
• Fixed an issue where cloning an experiment doubled plate-related tags

- Jennifer

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Release Notes for Cytobank 2.3 – 2.3.1.2
Published on: Feb 8, 2011 @ 17:16

Is it February already? We’ve made a number of updates in the last month. Here’s a summary of the new features and bug fixes included in the most recent Cytobank releases.

New Features

• New statistic has been added: Percentile Distance (5 to 95)
• The total file size for an experiment is now shown on the success page after experiment files are uploaded
• Files now filter on the tube name in an annotation dimension (e.g. conditions), when before they only filtered on the file name

Bug Fixes

• Sharing illustrations no longer creates extraneous illustrations for the original user
• Plot tables now show up only at the bottom of each illustration (instead of between each row)
• Empty experiments that are part of a project no longer show up until files are added
• Experiments without FCS files can now be deleted from the upload files applet
• Plot statistics can now be turned off for histogram overlays
• Cloning an experiment now maintains the categorization of files (experiment, compensation, other)

We love getting feedback from our users! You can send us comments or questions by email, tweet, or the “Feedback” link in the footer of the application.

- Jennifer

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Release Notes for Cytobank 2.2.9 – 2.2.9.1
Published on: Jan 12, 2011 @ 15:26

Happy 2011 from the Cytobank Development Team. We hope your new year is getting off to a great start. Here’s a list of bug fixes included in the most recent Cytobank releases.

Bug Fixes

• Fixed an issue with cloning where cloning a full experiment did not clone reagent names
• Fixed an issue with cloning where cloning a full experiment did not clone the compensations for illustrations
• Fixed an issue where empty spaces in the plot layout prevented heatmaps and histogram overlays from rendering
• Fixed an issue with percent in gate statistic not working properly with tailored gates
• Fixed an issue that occurred while tagging an experiment that had just been reset
• Fixed an issue with gates where gates were still drawn when “Show Gates” was turned off and “Show Gate Statistic” was turned on
• Fixed an issue where uploading more files to an existing experiment would cause the progress bar to freeze during preprocessing of the data
• Fixed a redirect that caused an incorrect page to load after recategorizing files on the experiment upload page
• Channels are now automatically selected in an illustration after a full clone
• If a custom compensation matrix is deleted, all illustrations using that compensation matrix will have their compensation setting reverted to File Internal
• “Reset Experiment” now has  a confirmation message

As always, we welcome any feedback you might have. You can get in touch with us by email, Twitter, or the “Feedback” link in the footer of the application.

- Chris

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Release Notes for Cytobank 2.2.6 – 2.2.7.2
Published on: Dec 20, 2010 @ 15:27

We’re back just in time for the holidays with a summary of the past several Cytobank releases. We’ve been busy fixing bugs on the front-end, as well as making quite a few backend performance optimizations, which we hope will get you to your results even faster.

One cool thing about the new features listed below is that they were all requested by Cytobank users via the “Feedback” link in the footer of the application (you’ll need to be logged in to access the link).

New Features

• Created an initial version of an automatic compensation wizard
• Added an option to display number of events in a gate instead of percentage of events
• Added the ability to use tailored gates on histogram plots
• Added the ability to import gates and compensations from public experiments

Performance

• Database optimizations to speed load times for the experiment details page
• Javascript optimizations to reduce unnecessary work when making updates to an Illustration
• Backend optimizations to improve memory management

Bug Fixes

• Fixed an issue with receiving double success messages when an experiment is created
• Fixed an issue with experiment variable tags so that searching for tags is no longer case-sensitive
• Updated wording in welcome email to new users
• Added a better success message for “Reset Illustration” function
• Fixed an issue with auto-channel selection in CyTOF files that contain parentheses in the channel names
• Fixed an issue with projects with the same name created by different users
• Fixed an issue with “Reset Experiment” such that the action now properly deletes all compensations in that experiment

In closing, we love getting feedback from our users, be it positive or negative, so please send us an email, tweet, or use the “Feedback” link in the footer of the application. Send us a request and one of the next new features in Cytobank could be for you.

Happy Holidays from the Cytobank Development Team,

- Chris

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Release Notes for Cytobank 2.2.5

Published on: Oct 22, 2010 @ 16:40

Welcome to another post chronicling our ongoing feature development and bug fixing.

We’d like to highlight two new features of note in this latest release. The first is that we’ve fixed some caching/performance related bugs. Now, after you’ve opened an illustration for the first time, subsequent reloads should happen much more quickly. This should be very apparent when you start rearranging your dimensions. The second new feature of note is the ability to see the Percent in Gate of a selected gate’s events when compared to the selected/active populations in the figure dimension. This statistic was displayed only on the plots previously, but it can now be shown in the table of statistics below each plot group for easy cutting and pasting to other software.

New Features

• Add statistic to illustration: percentage of events in Selected Gate (when compared to parent/active population)
• Added a new filter option to the Inbox: “My uploaded experiments”
• Updated the options for Default Inbox Experiments Filter in the user profile to allow a choice of any available filter as the default
• Added optional Location, Company/Organization, and “How did you find out about Cytobank?” fields to the registration form

Bug Fixes

• Fix for a display issue in the Gating Hierarchy
• Fix for a failure when trying to export VERY large experiments
• Fix for gating applet plot choice behavior when using histogram overlays or heatmaps in the illustration
• Fix for range gates not displaying on histograms in the illustration view
• Fix for PDF generation not working when FCS files contain quotes in the filename
• Fix to make sure all compensation matrices are copied over when exporting gated data to a new experiment
• Fix for an error caused when an upload attachment is clicked with no file selected
• Fix for an error in the Top Channels list when a user has no experiments
• Fix for a performance issue that caused unnecessary calculations to happen when building an illustration

As always, you can contact us via email, twitter, or the feedback link on the site, to ask questions or leave feedback.

- Chris

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Catching up on Release Notes (Cytobank 2.2.4)
Published on: Oct 5, 2010 @ 17:05

It’s been awhile since we posted release notes about the latest fixes and new features on Cytobank. In the time since the last post we’ve actually done a combination of 12 major and minor releases. So instead of posting every detail, which would take many pages, here is a summary of the changes that are the most visible to our users.

New Features

• Added the display of a table of statistics for all plot types and enabled related statistics controls
• Added “log base 2″ equation to the Plot Statistics: Equation menu
• Added “Transformed Median” and “Arcsinh Median” options to the Plot Statistics: Statistic menu
• Added a field so that users select “Percentile” and type in a value from 1-99 now instead of just having “95th Percentile” as the only option
• Added “Heat Plots” (pseudo-3D mountain plots) to the Plot Type
• Added Z-axis plot control for use in Heat Plot Mode
• Added “reset working illustration” button to the Experiment Summary page so the user doesn’t have to load their Working Illustration in order to reset it.
• Added a button to create a new experiment from gated FCS files, useful for de-barcoding experiments
• Improved IE8 support
• Added the ability to view the gating hierarchy for all files at once (as opposed to one file at a time)
• Added a setting to default the Inbox view to “My Experiments”

Bug Fixes

• Fixes to histogram overlay compensations
• Fixed caching bugs
• Fixed issue with dragging labels in layout placeholders
• Fixes to PDF support
• Fixed caching of illustration page tabs
• Fixes to prevent compensations being locked in
• Fixes to make sure uploaded compensations are available in the gating applet
• Fixed a bug with negative event counts for files with extremely large numbers of events
• Fixes related to gate and population deletion
• Fix to make sure illustration images are correctly updated when plot scales are changed
• Fix to “Check Gates” in the gating applet. It was displaying incorrect populations in some cases
• Fixes to scales when adding new files to an existing experiment that contains FCS Files from the CyTOF mass cytometer
• “Save Illustration” now redirects back to the Experiment Summary page on success, preventing extra illustration reload, helpful for very large illustrations
• Optimizations to speed up the loading of the annotations pages (Conditions, Timepoints, etc.)
• Optimizations to speed up the loading of the experiment summary page
• Updated instructions for how import a Flowjo compensation file
• Lots backend memory/performance optimizations (still very much ongoing!)

We hope that this was an informative summary about all the latest and greatest changes to Cytobank and that the new features will be useful to you. We’ve got plenty of new features queued up, as well as cleanup of existing functionality, so stay tuned. We love getting feedback from our users, be it positive or negative, so please send us an email, tweet, or use the “Feedback” link in the footer of the application.

- Chris

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Our Latest Software Release (2.1.4)

Published on: Apr 23, 2010 @ 20:18

This evening we released Cytobank version 2.1.4 to our production servers.

Here’s a summary list of the major changes and fixes:

• Added a post-logout page to provide users with a link to logout from their OpenID provider
• Added the ability to add experiments to a project from the “edit project” page
• Added the Top Channels and Experiment Variables filters to the left menu of the Inbox page
• Added support for importing FlowJo compensation files
• Added Log2 Ratio as another comparison equation for heatmap and histogram overlay illustrations
• Updated the Plate Dimension in the illustration to be populated with the value from keyword PLATE NAME instead of PLATE ID
• Updates to make detection of data files from CyTOF machines more accurate
• Bug fixes related to both importing/exporting compensations and creating compensations in Cytobank

We always try to incorporate user feedback into our development priorities so please leave comments here or email us.  We’re always listening and happy to hear about both the good and bad so we can continue to improve Cytobank.

- Chris