|Getting Started||Create a new project, add Prokka annotations and download the map image.|
Proksee makes it easy to go from sequence to publication-quality maps. Proksee projects can be started with a genome sequence, sequencing reads or a CGView.js JSON file. Once a project has been started, you will be taken to the Project Page where you can begin to annotate your genome and edit your map.
On the New Project page choose the tab for the type of data you have: Genome, Reads, or JSON. In addition, there are several examples.
A complete genome sequence in the Genbank, EMBL, or FASTA file formats. Sequences must be between 1,000 and 10 million bases long. The total number of contigs must be less than or equal to 1000. If you have a longer sequence that you would like to make into a map, send your sequence to Proksee Info. However, please note that longer sequence maps may be slow and difficult to work with.
An NCBI accession can be provided instead of a genome file. Accession IDs must be for complete GenBank records with sequence data.
Any features present in the GenBank or EMBL file will be automatically added to the map.
Raw sequencing reads can be provided as 1 or 2 FASTQ files. Each file can be optionally compressed and must be less than 1 GB. Only the following file extensions are allowed: fastq, gz, or zip.
To save space on the servers, uploaded read files will be deleted after the assembly is complete. A summary of the read files will be saved with the project for future reference.
Previously saved CGView.js JSON files can also be loaded. See Download - JSON for how to create these files.
There are several examples on the New Project page including a bacterial map, a plasmid and a map with contigs. Each example is run with a GenBank file using the accession ID indicated.
The My Projects page shows tables of your known projects. There are 2 types of projects: Session and User.
Session projects are created if you are not logged in. Anyone with the project ID (e.g. 121bc0d4-1b66-469c-a8c6-2aaf9ab9cadc) can access a session project. Session project IDs are stored locally and specifically with the client that started the project. So if you start a project on one browser (e.g. Chrome) it will not be automatically available on another browser (e.g. Safari).
Session projects are deleted 7 days after the Last Save Date. In addition, any jobs associated with a session project are deleted 7 days after they were started, regardless of the project Last Save Date. To save a project go to the project page, make a small change to the map and click Save Changes at the top of the page.
User projects are created if you are logged in. User projects will be available on all devices and browsers as long as you are logged in. Unlike session projects, user projects can not be shared.
Once you have an account, you can claim a project and add it your account. Go to My Projects on the browser/computer where the session project was created. Click Claim beside the project and it will be added to your user projects.
User account on Proksee are completely optional. One of the advantages of having an account are that your user projects will be easily available on other devices and browsers. In addition, your user projects will not be deleted after 7 days.
On your account page you can change your name, email and password. You can also completely delete your account and associated projects and jobs.
All user accounts come with 200 MB of storage. We may increase this quota over time as more resources become available.
Proksee does not automatically save map changes to the server. When you make any changes to your map the Saved button will change to Save Changes. Click the button and your changes will sync to the server.
If you were to reload the project page before saving any changes, the previously saved version of your map will be loaded. This allows for a basic way to undo changes.
As a precaution, Proksee will warn you when you are about to leave the page without saving.
The About Tab shows an overview of your project.
|About Tab Properties|
The name of the project. This can be changed at the top of the Project Page.
The ID for the project and map.
The date and time the project was created.
The date and time the project was last saved. This date is used to calculate when to delete old session projects.
The total size of the project, including all the jobs.
The total length of the map sequence. If any contigs have been marked as invisible, then both the total and visible length will be shown.
The number of contigs in the project. If any contigs have been marked as invisible, then both the total and visible number will be shown. Clicking on the contig count will open the Contig Panel.
The number of features in the project. Clicking on the feature count will open the Feature Panel.
The number of plots in the project. Clicking on the plot count will open the Plot Panel.
The source of the data used to create the project: genome, reads, json, example, tutorial, api
The project level genetic code. This is used as the default when translating proteins.
The Map Tab shows the genome map for the current project using the CGView.js browser. Above the map and to the left is the project ID (e.g. 121bc0d4-1b66-469c-a8c6-2aaf9ab9cadc).
The map viewer is the large rectangle area containing the map. The viewer will take up as much space as is available in the browser window. The viewer is surrounded by the Location Bar, Format Bar and Control Bar. Most of the settings to customize the look of the map are found in the Sidebar under the Display tab.
Use the mouse scroll wheel to zoom directly on the map. The zoom position is based on the mouse location.
Click and drag to move/pan the map position.
Clicking an element (e.g. feature, captions, legend items) will open the corresponding panel in the Sidebar and open the details for the element.
Hovering over an element (e.g. feature, contigs, plots) will show a popup with information for that element.
If a legend is displayed, the color swatches can be clicked to bring up the Color Picker.
Above the map and to the right is the Location Bar:
This bar shows the zoom level and position in base pairs of the current map. Clicking the Mark button will create a Bookmark. How the current position is determined depends on the map format:
- Linear: the position on the backbone that intersects with the vertical line going through the center of the map canvas.
- Circular: the position on the backbone that intersects with the radial line going through the center of the map and the center of the canvas.
The control bar is located on the middle-right side of the map. It contains controls for moving around the map.
|Control Bar Buttons|
[ . ] Reset the map position and zoom level.
[↓] Zoom in on the map.
[↑] Zoom out on the map.
[→] Move clockwise/right along the map.
[←] Move counter-clockwise/left along the map.
The format bar is located on the upper-right side of the map viewer. It contains controls for altering the overall map format.
|Format Bar Buttons|
[ / ] Set the map format to circular.
[ / ] Set the map format to linear.
Invert all the colors on the map.
Toggle the legend on/off.
Toggle the default labels on/off. (Best for maps with many evenly distributed labels)
Toggle the angled labels on/off. (Best for maps with fewer labels or with labels that are clustered together)
Lock the aspect ratio of the map to a square.
The Tool Panel contains a list of available tools that can be used to annotate or analyze your project. There are 2 types of tools: client-based and server-based.
|Tool Panel Properties|
Short description of the tool.
This is the software and version number for any external software packages used in this tool. Clicking on this will open the software home page in a new tab.
Citation to use for external software packages. Clicking on this will open the publication in a new tab.
The internal Proksee version for this tool. This will change with software package updates as well as any changes to the Proksee wrapping code. Clicking on this will open the tool summary page in a new tab. The summary includes the change log.
Client-based tools are run directly on your computer. To run a client-based tool:
- Click the Add button beside the tool name.
- Choose the appropriate settings in the dialog.
- Click the OK button.
The tool will immediately add the results to your map. However, remember that you still have to Save Changes or the results will be lost when reloading the page.
Server-based tools are run on the Proksee server as jobs. To run a server-based tool:
- Click the Start button beside the tool name.
- Choose the appropriate settings in the dialog.
- Click the OK button.
The tool will be submitted to the job queue on Proksee. Job progress and results are found in the Job Panel (Sidebar). To add the results to your map when the job is complete:
- Click the button beside the job name.
- Choose the appropriate settings in the dialog.
- Click the OK button.
Remember that you still have to Save Changes or the results will be lost when reloading the page. You can readd the results with the button.
Jobs are the result of running server-based tools. The results of jobs can be added to the map using the button. The button will expand the job into it's own Job Tab to show additional details including the job Files, Log and Data Cards.
|Job Panel Buttons|
Refreshes the list of job. This is not normally needed, however, if you expect to see jobs in the list and there are none, try clicking this button.
Brings up a dialog to add the results to the map.
Expands the Job to a new Job Tab in the Project Tabs list.
Marks this job as a favorite. Favorited jobs will automatically have their Job Tab open the next time the project page is loaded.
Deletes this job from the server. Note that the CGView Builder jobs can not be deleted.
|Job Panel Properties|
The name for this job. Click on the name to edit it.
One of the following: queued, running, complete or failed. Job are typically done in minutes but some may take hours. If your job has been queued or running for longer than 24 hours, or if you keep getting an error, please Contact Us with the Project ID, Job ID and a description of the problem.
Total size of the job.
The job ID. Provide this ID and the project ID when contacting support.
|Feature Source ID|
The source prefix added to any features created from this job. Each time features are added to a map from the same job, the number will increase (e.g. card-1.1, card-1.2). Clicking on the ID will open the Feature Panel and search for all features from this job.
The day and time this job was submitted.
The day and time this job started running.
The day and time this job finished running.
The time it took to run the job not including queue time.
The number of days before this job is deleted. Only shown for session projects.
The inputs used to run the job. This will include your settings from the dialog used to start the job.
Each Job Tab will have a Job Summary with details about the job at the top. These details are described in the Job Panel Properties table above. The Job Summary section can be collapsed by clicking the bar with the chevron at the top of the summary.
Below the summary is a collection of Job Cards.
Every job will have a Log Card. This is a close to real-time log of the job progress. If your job is stalled or has failed, the log may provide some answers.
Successfully completed jobs will have a Report Card which may have the following sections:
- Results: a count of the feature found by the tool and a button to add them to the map.
- Features Files: a list of files of interest with quick access buttons to view or download files. If a file is also used as the data source for a Data Card, a button to the Data Card will be available.
- Helpful Links: Links to external web pages with information about the tool.
- Citation: citation for the underlying software used in this tool. Please cite the software, if you use this tool for a publication.
- Some jobs may have additional data tables or plots
When a job is finished (either complete or failed), the Files Card will be available. This card shows all the input and output files for a job in a File Tree. From here, individual files can be downloaded or viewed with the File Viewer.
The File Tree lists all the job files. Folders can be open/closed by double clicking the row. Each row in the tree shows the name, kind (e.g. Text) and the size of the file or folder. For files, a button on the far right will download the file. Clicking on a file row will open it in the File Viewer. Multiple files can be selected by shift-clicking.
|File Tree Properties|
Download this file.
The File Viewer shows the selected file from the File Tree. If multiple files are selected, they can be quickly cycled through by clicking the and buttons.
The selected file will be displayed using the default kind/type for the file. The default kind is based on file extensions. File can be formatted differently by selecting a different format from the dropdown (e.g. text, code, csv, JSON, etc).
Some large files can cause issues when downloading to view them. To prevent this, only the first 100 KB of a file is downloaded. At the bottom of the viewer is a status bar which displays the number of lines and bytes downloaded. If the file is incomplete the status bar will have buttons to download More (ie. another 100 KB) or All (ie. the rest of the file). If the viewer stalls while viewing a large file, you may have to reload the page.
|File Viewer Properties|
Cycles backward and forward through the selected files. Only available when multiple files are selected.
Open the settings popup for the currently selected file type. This usually contains settings for fonts and other display options.
Opens the file viewer full screen, hiding the file tree.
Opens the file viewer to the bottom of the file tree.
Opens the file viewer to the right of the file tree.
Data Cards are tool specific. They may be formatted data table using one of the output files as the source. They may also be convenient shortcuts to specific output files. The bottom of each Data Card will contain the path to the file used as a data source.
This section describes some common controls found throughout Proksee
The Color Picker provides an interface for choosing colors. Click on the colored square to bring up the picker. The bar on the right picks the hue from 0° (bottom) to 360° (top). The square area lets you set the saturation from left (0%) to right (100%) and brightness from bottom (0%) to top (100%). The bottom bar is for the opacity.
The 2 squares on the bottom left show the previous color (left) and the current color (right). To undo the current color, click on the previous color (left square).
The Font control provides a simple interface for text styling.
One of the following font families. Note, that the actual font used will depend on your device and browser.
Style for the font. Bold, italic or both
Size of the font in pixels.
Proksee has a responsive design that works equally well on computers, phones and tablets. On smaller screens, the sidebar will automatically open and close as needed. For example, clicking the button beside a feature in the sidebar will close the sidebar and show the map zoomed into the feature. Clicking a feature on the map will open the sidebar, select the Feature Panel, and show the clicked feature.
To quickly open and close the sidebar, use the toggle strip on the left side of the sidebar. The toggle strip has a chevron on it. Chevrons can also be found in Job Tabs to shrink/expand areas.