Proksee - Help

Help Index
Proksee Overview
New Project
My Projects
User Accounts
Project Page
Map Tab
Sidebar Panels
Tool Panel
Job Panel
Miscellaneous

Tutorial Index
Getting Started	Create a new project, add Prokka annotations and download the map image.

FAQs
Answers to common problems/questions

Proksee Overview

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.

New Project

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.

New Project→Genome

Genome

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.

New Project→Reads

Reads

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.

New Project→JSON

JSON

Previously saved CGView.js JSON files can also be loaded. See Download - JSON for how to create these files.

New Project→Examples

Examples

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.

My Projects

The My Projects page shows tables of your known projects. There are 2 types of projects: Session and User.

My Projects→Session Projects

Session Projects

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.

My Projects→User Projects

User Projects

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.

My Projects→Claiming Projects

Claiming Projects

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 Accounts

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.

User Accounts→Storage Quota

Storage Quota

All user accounts come with 500 MB of storage. We may increase this quota over time as more resources become available.

User Accounts→User Menu

User Menu

When logged in, a User Menu will appear in the top-right of the page. This menu gives you a view of your current storage and the number of projects/jobs you own. There are also links here to logout as well as go to your account page.

Project Page

After a project is created you will be taken to the project page. This page shows your interactive Map and the Sidebar where many options and tools can be found. At the top of the page is the project name which can be edited in place.

Project Page→Saving Changes

Saving Changes

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.

Project Page→Project Tabs

Project Tabs

Under the project name is a set of tabs. The About and Map tabs are always present. Additional Job Tabs can be added by clicking the expand button for a Job.

Project Page→Project Tabs→About Tab

About Tab

The About Tab shows an overview of your project.

About Tab Properties
Name	The name of the project. This can be changed at the top of the Project Page.
Map	The ID for the project and map.
Created	The date and time the project was created.
Updated	The date and time the project was last saved. This date is used to calculate when to delete old session projects.
Project Size	The total size of the project, including all the jobs.
Sequence Length	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.
Contig Count	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.
Feature Count	The number of features in the project. Clicking on the feature count will open the Feature Panel.
Plot Count	The number of plots in the project. Clicking on the plot count will open the Plot Panel.
Source	The source of the data used to create the project: genome, reads, json, example, tutorial, api
Genetic Code	The project level genetic code. This is used as the default when translating proteins.

Map Tab

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).

Map Tab→Viewer

Viewer

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.

Viewer Controls
Zoom	Use the mouse scroll wheel to zoom directly on the map. The zoom position is based on the mouse location.
Pan	Click and drag to move/pan the map position.
Click	Clicking an element (e.g. feature, captions, legend items) will open the corresponding panel in the Sidebar and open the details for the element.
Hover	Hovering over an element (e.g. feature, contigs, plots) will show a popup with information for that element.
Color Picker	If a legend is displayed, the color swatches can be clicked to bring up the Color Picker.

Map Tab→Location Bar

Location Bar

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.

Map Tab→Control Bar

Control Bar

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.

Map Tab→Format Bar

Format Bar

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.

Sidebar Panels

The Sidebar contains panels for customizing the look of the map (Display); investigating features, plots and contigs on the map (Regions); downloading images, JSON and sequence (Download); starting annotation and analyses (Tools); and checking job results (Jobs).

The Sidebar can be closed to make more room for your map.

Sidebar Panel Buttons
	Close the Sidebar
	Open the Sidebar

See Responsive Design for how the Sidebar acts differently on smaller screens.

Sidebar Panels→Display

Sidebar Panels→Display→Tracks

Tracks

Tracks represent a set of features or a plot drawn on the map as one or more slots. Plot tracks are only drawn with one slot while feature tracks are drawn with 1, 2, or 6 slots depending on the Separate Features By option:

Option	Slots	Description
None	1	All features are drawn on a single slot
Strand	2	Features are drawn separated by strand
Reading Frame	6	Features are drawn separated by reading frame

Track Features
Instead of explicitly stating which features are on a track, tracks describe the features they contain based on either their source, tags, or type. Features can have one type, one source and multiple tags. Use the Track Contents option to choose what method (e.g. source, tag, type) and what value(s) to use when selecting features for a track. For example:

Method	Values	Features selected for the track
type	CDS	All the features with type equal to CDS
source	card-1.1	All the features with source equal to card-1.1
tag	low	All the features with a tag equal to low
tag	low, med	All the features with a tag equal to low OR med

Track Buttons
	Add a new Track.
	Track is visible or not visible.
	Delete the Track. A dialog will provide options to delete features and/or legends that are exclusive to the track being deleted.

Track Properties
Name	The name of the track.
Position	The position of the track relative to the backbone: Both: the forwards strands/slots will be on the outside of the backbone while the reverse strands will be on the inside Inside: all the strands/slots will be on the inside of the backbone. Outside: all the strands/slots will be on the outside of the backbone.
Separate Features By	Method for separating features onto track slots: None: The features are not separated and all appear on 1 slot. Strand: The features will appear on 2 slots. One slot each for the forward and reverse strands. Reading Frame: The features will appear on 6 slots. One slot each for each reading frame.
Size Ratio	The size ratios all depend on each other. For example: If all the track ratios are the same then all the track slots will be the same width. If one track has a ratio of 2 and all the others are 1, then it will be 2 times wider than the others. If one track has a ratio of 2 and all the others are 0.5, then it will be 4 times wider than the others.
Track Contents	This track contains features with a source, type or tag equal to one of the provided values. See Track Features for details and examples.
Number of Features/Plot points	The number of features or plot points that this track contains. Clicking the count will take you to the Feature Panel.

Sidebar Panels→Display→Legend

Legend

The legend consists of the legend as a whole and a set of legend items. The legend (as well as captions) can be placed on the canvas or the map:

Legend/Caption Positions
Map	Items placed on the map are not static and move when the map is panned or zoomed. The map position is based on the Length Percent of the genome sequence (e.g. 50% would be at the map half way point) and the Offset is a distance from the map. Positive Offsets indicate a distance from the outside ring of the map while a negative Offset indicates a distance from the inner ring of the map.
Canvas	The canvas is static and can be thought of as the window through which the map is viewed. Items placed on the canvas do not move when the map is panned or zoomed. The canvas position can be quickly set by clicking one of the areas in the 9 rectangle grid (e.g. upper-left). Fine tuning of the position can be done with the X/Y Percent inputs.

Legend Buttons
	When the legend is positioned on the map, this button will move the map to show the legend. This button does not appear when positioned on the Canvas.
	Track is visible or not visible.

Legend Properties
Position	Where to place the legend. See Legend/Caption Positions for details. Canvas: Legend is static and does not move. Map: Legend moves with the map.
Anchor	The anchor point describes where the position attaches to the legend/caption bounding box.
Default Font	The default font to use for the legend items. Individual items can override this value. The alignment buttons will align the all the legend items: Left: the color swatches will be on the left Right: the color swatches will be on the right
Default Font Color	The default color to use for the legend items. Individual items can override this value.
Default Minimum Arc Length	The default minimum arc length to use for the legend items. Individual items can override this value. Features are drawn based on their length and therefore small features (e.g. 1 bp) can appear invisible on maps depending on the zoom level. By setting a minimum arc length, small features will be more visible and be darker on the map.
Background Color	The color to use for the legend background.

Sidebar Panels→Display→Legend→Legend Items

Legend Items

Legend items are associated with features or plots. Features and plots will be drawn using the legend item color. Features will also be drawn using the legend item decoration.

Decorations
	Draw features as arrows. The arrow head length can be adjusted LINK.
	Draw features as arcs
	Draw features as arcs with the width of the arc set to the feature score. The score should be between 0 and 1, where 0 would be 0 width and 1 would be full width. If no score is associated with the feature it will be drawn full width.
	Do not draw features

Legend Item Buttons
	Add a new legend item.
	Legend item is visible or not visible.
	Delete the legend item. A dialog will provide options to delete features and/or plots that are exclusive to the legend being deleted.

Legend Item Properties
Name	The name of legend item as it will appear in the legend. Names must be unique.
Color	The color to use when drawing features or plots with this legend item.
Decoration	The decoration to use when drawing features. See Decorations table. Arrow - Draw features as arrows. Arc - Draw features as arcs. Score - Draw as arc with width based on feature score (0-1). None - Do not draw feature.
Font	The font to use for this legend item. The font options will be faded, if the default is being used. If changed, this value will override the default. Click the Default button to use the Legend default.
Font Color	The font color to use for this legend item. The font color will be faded, if the default is being used. If changed, this value will override the default. Click the Default button to use the Legend default.
Minimum Arc Length	Features are drawn based on their length and therefore small features (e.g. 1 bp) can appear invisible on maps depending on the zoom level. By setting a minimum arc length, small features will be more visible and be darker on the map. The minimum arc length will be faded, if the default is being used. If changed, this value will override the default. Click the Default button to use the Legend default.

Sidebar Panels→Display→Captions

Captions

Captions are boxes of one or more lines of text that can be placed anywhere on the map or canvas.

Caption Buttons
	Add a new caption.
	When the caption is positioned on the map, this button will move the map to show the caption. This button does not appear when positioned on the Canvas.
	Caption is visible or not visible.
	Delete the caption.

Caption Properties
Caption Text	The text to display as a caption on the map. Multiple lines of text can be used.
Position	Where to place the caption. See Legend/Caption Positions for details. Canvas: Caption is static and does not move. Map: Caption moves with the map.
Anchor	The anchor point describes where the position attaches to the legend/caption bounding box.
Font	The font to use for the caption. The alignment buttons only matter when using multiple lines of text.
Font Color	The color to use for the caption.
Background Color	The color to use for the caption background.

Sidebar Panels→Display→Settings

Settings

The settings are for the appearance of several map components including the Labels, Rulers, Backbone, Dividers, and Sequence.

Setting Buttons
	This selected map component (e.g. labels, ruler, backbone, dividers, sequence) will be visible/invisible.

Sidebar Panels→Display→Settings→General

General

General settings for the overall amp.

General Properties
Background Color	The background color for the map.
Show Feature Shading	With feature shading on, features and the backbone are drawn with a slight bevel effect to add 3D depth.
Arrow Head Length	The length of the arrow on features that have the Arrow decoration. The length is based on the feature width and can range from 0 (no arrowhead) to 1 (the arrowhead is as long as the feature is wide).
Initial Map Thickness	The initial thickness of the map at a zoom level of 1. This value is a proportion of the canvas size. For circular maps, this is defined as the proportion of the smallest canvas dimension. For linear maps, it's the proportion of the canvas height. This value is ignored if the maximum map thickness is smaller.
Maximum Map Thickness	The maximum thickness of the map when zoomed in. This value is a proportion of the canvas size. For circular maps, this is defined as the proportion of the smallest canvas dimension. For linear maps, it's the proportion of the canvas height.

Sidebar Panels→Display→Settings→Labels

Labels

Settings for the feature labels.

Label Properties
Color	The font color to use for all the labels. The default is to use the same color as the feature's current legend.
Font	The font to use for the labels.
Only Favorites	If set to Yes, then only features marked as favorites will have labels.

Sidebar Panels→Display→Settings→Ruler

Ruler

Settings for the map ruler. The ruler appears on the inner and outer ring of the map as a series of tick marks. The inner ring also contains the tick labels.

Ruler Properties
Color	The color to use for the ruler lines and text.
Font	The font to use for the ruler labels.

Sidebar Panels→Display→Settings→Backbone

Backbone

Settings for the map backbone. The backbone represents the map sequence. It is either drawn as a solid line or as a set of contigs.

Backbone Properties
Color	The color to use for the backbone.
Alternate Color (Contigs)	If contigs are present, this is the color for alternating contigs.
Thickness	The thickness/width of the backbone. The backbone will automatically get thicker when zoomed in to show the sequence.
Decoration	The decoration to use when drawing contigs: Arrow - Draw contigs as arrows. Arc - Draw contigs as arcs.

Sidebar Panels→Display→Settings→Dividers

Dividers

The dividers appear in between tracks and slots. The dividers can be mirrored meaning that both the slot and track dividers will use the same settings. If mirroring is off, tracks and slots will use separate dividers.

Divider Properties
Color	The color to use for the divider.
Mirror	Turn on/off divider mirroring: On: use same settings for track and slot dividers. Off: use different settings for track and slot dividers.
Thickness	The thickness of the divider.
Spacing	The spacing between the slot/track contents and the divider.

Sidebar Panels→Display→Settings→Sequence

Sequence

Settings for the map sequence. The sequence will appear in the backbone when zoomed in enough.

Sequence Properties
Color	The color to use for the sequence.
Font	The font to use for the sequence.

Sidebar Panels→Regions

Sidebar Panels→Regions→Contigs

Contigs

The Contigs Panel lists the contigs in the project genome. This may be a single sequence.

Contig Buttons
	Move and zoom to focus on this contig.
	Contig is visible or not visible. At least one contig must be visible.
	Delete the contig. If there is only one contig, it can not be deleted.

Contig Properties
Name	The name for the contig. Contig names must be unique. As contig names may be used when running tools, changing the contig name may affect job results.
Order	The order of the contig in relation to the other contigs. Changing this number will move the contig around the map. All the features associated with the contig will move with it.
Orientation	The direction of the contig. Flipping the orientation will also flip the features on the contig.
Color	By default contigs will use the Backbone color and alternate color. Change this value to make a contig stand out.
Features	The number of features on this contig. Clicking on the feature count will open the Feature Panel.

Sidebar Panels→Regions→Features

Features

The Features Panel lists all the features in this project. Features can be on one or more tracks. Tracks state which features to include based on either the feature source, type or tags. See Track Features for details.

Feature Buttons
	Add a new feature.
	Mark this feature as a favorite. This can be useful when combined with the Labels - Only Favorites setting.
	Move and zoom to focus on this feature.
	The feature is visible or not visible.
	Delete the feature.

Feature Properties
Name	The name for the feature.
Type	The feature type (e.g CDS, tRNA, rRNA). If the project was started with a GenBank file, the type will be same as the feature key. Feature keys are described in detail here. To create a new type, check the feature's checkbox and then click the edit (pencil) button.
Legend	The Legend to use when drawing this feature. The legend describes the feature color and decoration.
Start	The start position (bp) in relation to the contig the feature is on.
Stop	The stop/end position (bp) in relation to the contig the feature is on.
Strand	The strand the feature is on.
Length	Length of the feature.
Score	Score associated with the feature. This is a number between 0 and 1. The score can be used by the legend decoration to alter the feature width.
Source ID	The Source ID is added to the feature by the tool that created the feature. This provides an easy way to add all the features created by a tool to a track.
Contig	The contig this feature is on. If the project contains multitple contigs, this contig can be changed to a different contig. Warning: if the feature position will not fit within the selected contig, the feature start/stop will be altered to fit.
Tags	Tags are a simple way to label or group features. Multiple tags are allowed.
Tracks	A list of the Tracks this feature is currently on. Clicking the track name will open the appropriate track.

Sidebar Panels→Regions→Plots

Plots

The Plot Panel will list all the plots in this project.

Plot Buttons
	Add a new plot. Brings up the dialog for the Plots tool.
	Mark this plot as a favorite.
	The plot is visible or not visible.
	Delete the plot.

Plot Properties
Name	The name for the plot.
Legend (Above Baseline)	The Legend to use when drawing the plot above the baseline.
Legend (Below Baseline)	The Legend to use when drawing the plot below the baseline. Setting this to Same as Above will result in a single color for the plot.
Baseline	The baseline for the plot. The plot is filled with the appropriate legend color from the plot value to the baseline.
Axis Min	The minimum value to use for the axis. This number can not be greater than the minimum value.
Axis Max	The maximum value to use for the axis. This number can not be less than the maximum value.
Number of Values	The number of points along this plot.
Minimum Value	The minimum value of this plot.
Maximum Value	The maximum value of this plot.
Mean Value	The average value of this plot.
Median Value	The median value of this plot.
Source ID	The Source ID is added to the plot by the tool that created the plot.
Tracks	A list of the Tracks this plot is currently on.
Type	The plot type. There is currently only the line type.

Sidebar Panels→Regions→Bookmarks

Bookmarks

Bookmarks are a convenient way to save regions of interest on the map. Bookmarks can be created by either clicking Mark in the Location Bar or the button. The new bookmark will be for the current map position, zoom level and format.

Bookmark Buttons
	Add a new bookmark. The Mark button in the Location Bar can also be used.
	Move and zoom to the bookmark's saved position. Depending on the bookmark, the map format may also change.
	Delete the bookmark.

Bookmark Properties
Name	The name for the bookmark. Defaults to Bookmark-n, where n is an incrementing number starting with 1.
Shortcut Key	A single keyboard key that when pressed quickly moves to this bookmark. By default, bookmarks will assigned numbers: 1, 2, 3, etc
Format	The map format: Linear or Circular
Position	The map position in base pairs.
Zoom	The zoom level.
Backbone Offset	A zero offset means the map should be centered on the backbone. Positive and negative values move the backbone from the canvas center.

Sidebar Panels→Download

Sidebar Panels→Download→Image - PNG

Sidebar Panels→Download→Image - SVG

Sidebar Panels→Download→JSON

Tool Panel

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.

Type	Button	Summary
Client	Add	Run on your computer One step process
Server	Start	Run as a job on the Proksee server Two step process

Tool Panel Properties
Description	Short description of the tool.
Software	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	Citation to use for external software packages. Clicking on this will open the publication in a new tab.
Version	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.

Tool Panel→Client-Based Tools

Client-Based Tools

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.

Tool Panel→Server-Based Tools

Server-Based Tools

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.

Job Panel

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
Name	The name for this job. Click on the name to edit it.
Status	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.
Size	Total size of the job.
Id	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.
Created	The day and time this job was submitted.
Start Time	The day and time this job started running.
End Time	The day and time this job finished running.
Run Time	The time it took to run the job not including queue time.
Days Left	The number of days before this job is deleted. Only shown for session projects.
Inputs	The inputs used to run the job. This will include your settings from the dialog used to start the job.

Job Panel→Job Tabs

Job Tabs

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.

Job Panel→Log Card

Log Card

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.

Job Panel→Report Card

Report Card

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

Job Panel→Files Card

Files Card

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.

Job Panel→Files Card→File Tree

File Tree

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.

Job Panel→Files Card→File Viewer

File Viewer

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.

Job Panel→Data Cards

Data Cards

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.

Miscellaneous

Miscellaneous→Common Controls

Common Controls

This section describes some common controls found throughout Proksee

Miscellaneous→Common Controls→Color Picker

Color Picker

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%). Directly below the large square is the opacity bar with the current opacity (0-100%) shown on the right.

Under the opacity bar are the Hex and RGB values for the current color and below that are a selection of color swatches. The swatches are paired so that the bottom swatch is a darker version of the top.

The last row of swatches are favorites. Click on the star to add or remove a favorite. Favorites are saved in the browser and will be available the next time you open the color picker.

The 2 squares in the top middle show the previous color (left) and the current color (right). To undo the current color, click on the previous color (left square).
The button in the top left switches modes between the HSV/RGB color picker and a selection of predefined color swatches.

Color Picker Tips

The R, G, and B labels can be dragged left and right to change the value. This is useful for fine tuning the color.
As a shortcut, the Hex input can take a variety of different color values (see examples below). After entering a value, hit Return or click outside the input to update the color.
- Hex code (with or without the #): #AAA, BCD, #A1B4C8, BB88CC
- rgb(a) strings: rgb(255, 0, 0), rgba(255, 0, 0, 0.5)
- Named colors (see list): red, blue, green, LightCoral, SteelBlue

Miscellaneous→Common Controls→Font

Font

The Font control provides a simple interface for text styling.

Font Properties
Family	One of the following font families. Note, that the actual font used will depend on your device and browser. Sans Serif: plain font that has no "serifs" (ie. the little strokes on the end of the letters). Serif: font with "serifs" (ie. the little strokes on the end of the letters). Monospace: font where each character and space has the same width.
Style	Style for the font. Bold, italic or both
Size	Size of the font in pixels.

Font Properties

Family

One of the following font families. Note, that the actual font used will depend on your device and browser.

Sans Serif: plain font that has no "serifs" (ie. the little strokes on the end of the letters).
Serif: font with "serifs" (ie. the little strokes on the end of the letters).
Monospace: font where each character and space has the same width.

Style

Style for the font. Bold, italic or both

Size

Size of the font in pixels.

Miscellaneous→Responsive Design

Responsive Design

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.