To create an account for ImmPort Galaxy, click on 'User' in the top green bar. Click on register, and enter your email address and password. Choose a public name and you're good to go. More here.
Note that registration to ImmPort Galaxy is separate from registration to ImmPort.
Creating an account allows users to keep their histories (uploaded and generated files). Having an account also allows users to access and use workflows. You can use ImmPort Galaxy without registering, but your work will not be saved.
A 20Gb quota is enforced for each user. To stay within the limits of the quota, users are invited to delete and purge data they do not wish to keep. Data will be kept for a year. ImmPort is not responsible for data corruption that may occur on the ImmPort Galaxy server. If your data is important, please download the files on your local machine.
This policy is subject to change.
To access available interactive tours of Galaxy, click on 'Help' in the top green bar. Click on interactive tours and pick the tour you want to take.
To enable scratchbooks, click on the square icon next to 'User' on the top green bar. In scratchbook mode, several files can be viewed at the same time. More here.
To upload data, click on 'Upload file(s)' in the 'Upload Flow Files' section at the top of the left panel. Files can be selected from your computer by clicking on 'Choose local file', or dragged and dropped into the upload dialog box. 'Paste/Fetch data' gives the option to either directly copy the content of a file, or to retrieve data through a URL. More info here.
ImmPort Galaxy supports standard text formats (plain text, csv and tsv/tabular), FCS 2.0 and 3.0, pdf and HTML. Files generated by ImmPort Galaxy are FCS 3.0, text or HTML.
Note that the extension of the text files generated by ImmPort Galaxy are non-standard and might not be understood by your computer once downloaded. You can change their datatype to 'txt' by editing their attribute (click on the pencil icon next to the file name to access that option) before download, or rename the file once downloaded. Alternatively you can set your local file browser to open that type of file with your favorite text editor.
Text files generated by ImmPort Galaxy have non-standard extensions, but they are still text files. Once downloaded, they can be read and opened by your favorite text editor, or with excel as tab-separated text.
Files in the history panel can be grey, green, yellow or red. Grey indicates that the job is being evaluated or queued to run, yellow that the job is running. Green indicates that the job completed successfully. Red indicates a problem with the job. For more info on how to proceed with a failed job, see Troubleshooting / ImmPort Galaxy tool issues. More info here.
To delete files, click on the 'x' next to the name of the files to delete. To delete the file permanently (or "purge"), show deleted files in your history, and click on 'Permanently remove it from disk' in the yellow box below the name of the file to purge. Once permanently deleted, a file is NOT recoverable.
Deleted files can be recovered, within the limits of the data retention policy. To recover a deleted file in a history, click on 'deleted' at the top of your history. The link will now read 'hide deleted', and every file in your history that has been deleted will be displayed and highlighted with a yellow box. You can restore deleted files by clicking on 'undelete'. If a file has been deleted by the administrator because of the data retention policy, it will not be recoverable. Purged files or histories are NOT recoverable. More here.
To download files, start by clicking on the filename in your history. File details (file size, format...) will appear, along with a few grey icons at the bottom. Click on the first icon on the left (floppy disk) to download the file. HTML output files will be downloaded as a zip file containing all supporting data. Note that binary files will be downloaded automatically when you click on the eye icon next to their name.
Note that the graphs generated with Plotly in the visualization tools output can be saved as pngs by clicking on the camera icon that appears when mousing over the graphs. For the other graphs, a screenshot is the best option so far. More here.
For higher resolution images, please contact us.
The three visible icons next to each filename in the history panel allow users to visualize the file in the central panel, or download the file if it is not a format Galaxy can read (eye), to edit the metadata associated with the file (pencil) and to delete the file (x). Clicking on the filename displays file details and more icons. The far left one (floppy disk) controls file download. The second one (i) opens complete file and job details in the central panel. This is the one that gives you access to the actual command line used to run the job, and actual error messages if any (by clicking on 'stderr'). The next icon (circling arrows) brings up the tool view in the central panel and allows you to rerun the job that generated the file (with the same parameters already selected / entered). The fourth icon is not present in all files and allows access to different visualization options (see Visualization / Galaxy options). The last two icons allow users to add a tag or a comment to the file. More here.
Manage your analyses with dataset collections and histories.
A 'dataset' in Galaxy-speak is a single file. Once a file is loaded in Galaxy, it becomes accessible as part of your saved datasets, provided you are logged in. To access saved datasets, click on 'User' in the top green bar, then click on 'Saved datasets'. From the Datasets Management page, you can copy any of your existing datasets to your current history.
A 'dataset collection' in Galaxy-speak is a set of files grouped together on which you can run tools, instead of running each tool on each individual file. It's a powerful way to analyse data as it allows you to run the same job, with the same parameters, on many files at the same time while keeping track of each file. Some tools in ImmPort Galaxy require dataset collections as input. More info here.
To create a dataset collection, click on the checkbox at the top of your history. This will allow you to select files by clicking checkboxes. Once you have selected files that should go in a dataset collection, click on 'For all selected...' and select 'Build a dataset list' in the dropdown menu. More here.
Unless the input type is restricted, there are three icons next to each file input on the tool interface. The first one allows to select single files, the second one several files, and the third one dataset collections. To run jobs on dataset collections, click on the third icon. If there are no dataset collections in the history, nothing will appear in the dropdown. Otherwise, just select your dataset collection and run the tool as you would for a single file. More here.
Creating a history is only available once logged in. To create a new history, click on the cog icon at the top right of the right panel and select 'Create New'. You can also create a new history from the history view by clicking on the icon right of the cog, and clicking on 'create new' at the top right corner. More here.
Histories can be populated either by uploading data, or with files already uploaded or generated by galaxy tools in other histories. To move files from existing histories to a new history, go to the history view by clicking on the icon right of the cog at the top right of the right panel. Drag and drop existing files or dataset collections from existing histories into the newly created history. More here.
This feature is only available once logged in. Click on 'Shared Data' on the top green bar. Select 'Publish Histories' to see publicly available histories, and click on the one you want to import. On the next screen, click on 'Import history' at the top right corner. More here.
To keep track of your histories, rename them by clicking on their name on the right panel or in the history view. Hit enter once the new name is written to save it. Another option is to click on the cog icon at the top right of the right panel, select 'Saved Histories' and click on the downward arrow next to the history name to change. In the dropdown, select rename.
There are several ways to delete a history. Switch to the history that needs to be deleted, click on the cog icon at the top right of the right panel and select 'Delete' under 'History Action'. Alternatively, from any history click on 'Saved histories', select the history to delete and click 'Delete'.
Within the scope of the data retention policy, a deleted history is recoverable. To recover a deleted history, click on the square icon next to the cog at the top right corner in the right panel. In the history view, click on the ellipsis icon next to the search windows and select 'Include deleted histories'. All deleted histories should now be displayed with the others. Above the history that needs to be recovered, click on the downward arrow, and select 'Undelete'. More here.
Sharing histories is only available once logged in.
To share a history, click on the cog icon at the top right of the right panel and select 'Saved histories'. Click on the arrow next to the name of the history you want to share, and in the dropdown menu, select 'Share or Publish'. To share the current history, click on the cog icon and select 'Share or Publish'. Histories can be made publicly available via link or by publishing them to ImmPort Galaxy, or shared with another ImmPort Galaxy user only. More here.
ImmPort Galaxy tools all have a similar interface. The top section controls input file(s) and parameter(s) selection. Below that is a help section describing expected input and outputs. Citations are indicated at the very bottom if applicable. More here.
You are more than welcome to contribute to ImmPort Galaxy (or Galaxy!). Guidelines to write a galaxy tool can be found here.
To contribute your tool to ImmPort Galaxy, fork us on GitHub or contact us directly. To be added to ImmPort Galaxy, a tool should be up to current IUC standards. In addition, the help section should be complete with input and output file description.
Take it a step further by sharing your tool in the Galaxy toolshed. More info here.
ImmPort Galaxy provides a few basic analysis workflows which you can access by logging in. Currently available workflows support QC and basic flow analysis. Workflows created and maintained by the ImmPort team are published under 'immport-galaxy'.
To access or import available workflows, click on 'Shared Data' on the top green bar and select 'Published Workflows'. Click on the downward arrow next to the name of the workflow to import, and select 'Import'. Workflows are immediately available to use. Workflows created and maintained by the ImmPort team are published under 'immport-galaxy'. More here.
To use an existing workflow, click on 'Workflow' in the top green bar. Click on the downward arrow next to the name of the workflow to run and select 'Run'. Alternatively, click on 'All workflows' in the left panel under the tools, and click on the workflow to run.
Workflows can be added to the tool panel, under 'Workflows', for ease of use. To do that, click on 'Configure your workflow menu' after clicking on 'Workflow' in the top green bar. Select the workflows to display by checking the box under 'Show in menu'. The workflows should now appear under the list of tools in the tool panel. More here.
To create a workflow, click on 'Workflow' in the top green bar, then on 'Create new workflow' on the top right. Any of the tools in the tool panel are accessible from the workflow editor, and can be arranged in whatever order seems relevant. More here.
Workflows can be shared with specific users, or be made publicly available. To share a workflow, click on 'Workflow' in the top green bar. Click on the downward arrow next to the name of the workflow to share, and select 'Share or Publish'. More here.
To run a workflow, click on the name of the workflow. Once selected, you should see a list of the tools involved in the workflow. Select your input file(s) and any option or parameters in each of the tool. To start the job, click on 'Run workflow'. Generated files can be sent to a new hostory by checking the option at the bottom of the workflow. More here.
There are three input options for most tools in ImmPort Galaxy: single file, multiple file and dataset collection. The two latter options are not that different in that they both allow running a tool on several files at the same time. However using dataset collections makes it easier to keep track of your output files as they will also be grouped in a collection. Collections can be thought of as directories in which files (or dataset in Galaxy speak) are grouped.
Note that some tools expect a dataset collection as input.
The following steps are recommended to run a flow analysis using FLOCK in ImmPort Galaxy:
- Create a dataset collection containing all FCS files to gate / analyze.
- Transform, compensate and convert FCS files to text.
- Merge the files together into one reference file.
- Run the reference file through FLOCK to identify the different fluorescence intensity patterns defining each cell type in the data.
- Run each file from the original dataset collection through Cross Sample using the FLOCK result to attribute each event to a FLOCK-defined population.
- Explore the populations defined by FLOCK with the tool 'Generate overview information of reference set of clusters or populations' under 'Flow visualization tools'
- Explore the results of Cross Sample with the tool 'Generate overview information of a multi-sample analysis' under 'Flow visualization tools'
This workflow is available among the workflows published by immport-galaxy.
Feel free to contact us for additional information. More references are indicated here and at the bottom of the help section of each tool.
CyTOF data can be analyzed with FLOCK if enough files are concatenated together to satisfy the minimum number of events required for the clustering algorithm to detect patterns. Running FLOCK on too few events is not recommended.
ImmPort Galaxy currently supports two clustering algorithms, FLOCK and FlowSOM. Flock generates 'Populations' and FlowSOM 'clusters' and 'meta-clusters'. Those terms are interchangeable to refer to groups of events from FCS files with similar marker expression patterns - as deemed by the clustering algorithm.
The reference set overview has several tabs. The first one is a summary of the data. The following tab displays all scatter plots for all markers. The third and fourth tabs display interactive 2D and 3D scatter plots respectively. The parallel coordinate tab shows the relationship between each marker mean fluorescence intensity and populations or clusters defined by the clustering algorithm used. The next tab displays the distribution of MFIs per population and marker as a boxplot. The last tab is optional and only appears if the cell ontology is queried.
Find more details in the help section of the tool.
The multi-sample overview has several tabs. The first one is a summary of the data. The following tabs display the proportion of each population in each sample/file. The first parallel coordinate tab shows the relationship between samples/files and populations or cluster defined by the clustering algorithm, while the second one displays relationships between samples/files, markers intensities and populations. The last tab shows the MFI distribution per marker and population as a boxplot.
Find more details in the help section of the tool.
The visualization tools currently have an upper limit of 40 populations, or clusters.
If you find any issues with the Galaxy framework, please contact us with a summary of what you were doing and the error message you received.
The first thing to do if a tool's output turns red instead of the expected green is to read the exit message. To do this, click on the filename, and once the file details appear, on the 'i' icon at the bottom. In the central pane should now be all of the job's details. Click on 'stderr' to access the exit message. If that does not help, please copy the message and send it to us here.
Querying the cell ontology database with flowCL will not work with user-defined marker names. The marker names need to be in a format compatible with the CL. Things like 'CELL_LENGTH' or 'Time' will not be recognized. For more help, please contact us.
There are a few things you can do if your workflow doesn't run. If there been a new release recently, it's possible that the workflows need to be updated with the new tools. You can try re-importing the workflow, if appropriate. Alternatively, you can edit the workflow yourself with the workflow editor, see more here. If this doesn't solve your problem, please contact us.
In some cases, PDF might take some time to load. If refreshing your browser doesn't help, download the pdf and try to open it locally.
The 3D scatter plot in one of the visualization tool's output is supported by a plug-in called WebGL. Later versions of Chrome unfortunately do not support WebGL. If that is the case, try using another web browser such as Mozilla Firefox.
Yellow indicates that the program used to generate the file is still running. If you believe that it has been running for too long, one of the easy explanations is that the file name is too long and cannot be accomodated by the database. Try editing the name of your file(s) by clicking on the pencil icon next to the name of your dataset, and re-running the tool. If this doesn't work, please let us know.