Glossary

A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z

A

Admin permissions

Admin permissions allow users to modify another user's permissions on a project, add or remove people from the project and manage funding sources. They also have copy, write, and execute permissions.

Tip: You can view project members' permissions in the Project Members panel of the Project Dashboard.

See also: copy permissions, execute permissions, permissions, project, project dashboard, project member, read permissions, write permissions

Alias (volumes API)

An [alias](doc:aliases) is a pointer, on the Platform, that refers to a file in a cloud storage repository (AWS S3 bucket, or Google Cloud storage). Aliases enable files in cloud storage repositories outside the Platform to be manipulated on the Platform, for instance, to input them to computational tasks.

API

The [Seven Bridges API ](doc:the-api)(Application Programming Interface) is used to integrate the Seven Bridges Platform with other applications, and to automate most procedures on it, such as uploading files, querying metadata, and executing analyses.

API bindings

API bindings allow you to communicate with Seven Bridges Platform API using [Python](https://github.com/sbg/sevenbridges-python) and [R](https://github.com/sbg/sevenbridges-r).

App

Apps are bioinformatics tools and workflows. The Platform hosts many pre-built apps that are ready to use. They are put on the Platform and maintained by the Seven Bridges bioinformatics team. These apps can be executed on the Platform as is.

Tip: Public apps are available on the Platform, but you can also bring your own tools and design your own workflows.

See also: projectpublic appstoolworkflow

Archiving

[Archiving](doc:file-archiving-overview) is a process of storing files which you don't intend to use for longer periods of time (typically over three months). Archived files are billed at a significantly reduced price compared to data which is always available.

B

Batch tasks

The [batch task](doc:about-batch-analyses) feature of workflows allows you to run identical analyses on different data by entering multiple input files and grouping them with specified metadata criteria.

Billing Group

A billing group is a specific payment method used to fund storage and computations on the Seven Bridges Platform.

See also: project, project member

C

Copy permissions

Copy permissions allow users to view file content, copy, and download files from a project. Collaborators with copy permissions do not automatically have execute, write, or admin privileges.

Tip: You can view project members' permissions in the Project Members panel of the Project Dashboard.

See also: admin permissions, execute permissions, permissions, project, project dashboard, project member, read permissions, write permissions

Common Workflow Language (CWL)

The Common Workflow Language (CWL) is an open specification for describing data analysis tools and workflows. It was developed to enable portability of this software. The Tool Editor both reads and writes CWL tool descriptions. Likewise, the API returns app information in the CWL format.

A CWL description of a tool specifies details of its command line options, its input and output ports, and contains a reference to a Docker image on which the tool is installed.

Tip: You can use the CWL to describe tools and use the same tool across multiple platforms

See also: docker, sdk, Seven Bridges Image Registry, tool, tool editor

CCLE

The Cancer Cell Line Encyclopedia (CCLE) is a public project which contains large Open Access Files from the CCLE [which you can use on the Seven Bridges Platform](doc:ccle).

D

Data

Data is packaged as files and fed into workflows for analysis. Files are stored on the Platform in two repositories: Public Reference Files and Project Files.

See also: files, project, project files, public reference files

Docker

[Docker](http://www.docker.com) is a toolkit for creating and running software containers. Docker packages applications and their dependencies into discrete runtime environments "containers". This allows applications to run in diverse infrastructures. They're based on read-only environments called images.

Tip: Docker images are stored on the Platform in the Seven Bridges Image Registry.

See also: sdk, Seven Bridges Image Registry, tool, tool editor

Dynamic Expression

Dynamic expressions can be used in tool descriptions to create arguments that vary depending on features of the job, inputs, or outputs. Dynamic expressions are written in Javascript.

E

Execute permissions

Execute permissions allow users to execute workflows and abort tasks in a project. Collaborators with execute permissions do not automatically have copy, write, or admin privileges.

Tip: You can view project members' permissions in the Project Members panel of the Project Dashboard.

See also: admin permissions, copy permissions, permissions, project, project dashboard, project member, read permissions, write permissions

F

Files

Files are units of data fed into workflows for analysis. Files are stored on the Platform in two repositories: Public Reference Files and Project Files.

See also: data, project, project files, public reference files

File Tags

File tags are used on the Seven Bridges Platform as a way to annotate files (both public reference files and the ones within your project) with relevant information about their type or purpose. This can help you differentiate them more easily and allow you to filter files based on their tags. To learn more about file tags see: [Tag your files](doc:tag-your-files) and [Filter by tags](doc:tag-your-files#section-filtering-tags-within-a-project).

See also: data, project, project files, public reference files

G

Glob

A [glob](page:glob) is an expression used to specify a set of filenames that match a pattern. Globs use wildcard characters to define a pattern. For example: *.bam is a glob pattern that uses the * wildcard to match all files with the .bam extension.

Glob patterns are used in the Tool Editor to specify which files are reported as outputs on a tool's output port. A glob pattern can also be used to specify which files will be retrieved as log files when running a tool.

See also: data, project, project files, public reference files

I

Input

Inputs are data that is supplied to a tool.

Tip: Typically, inputs are files. However, if you are installing your own tool on the Platform using the SDK, then any parameters or settings that are supplied to the tool are treated as inputs and are accepted by their own input ports, which you should specify in the tool editor.

See also: input port, SDK, tool, tool editor

Input and Output Ports

A port is a "gateway" for data to flow in and out of your tool. You should add one input port per datatype your tool takes as input (such as files, strings, or integers) and per method of processing. For instance, if your tool takes a file and an integer as input per execution, you should enter two ports; if it takes two files, one reference and one data file, and does different things to each, then you should also enter two ports.

Tip:

  1. On the Workflow editor, a tool's ports are represented by circles on the node that represents the tool.
  2. Typically, input ports take data files. However, if you are installing your own tool on the Platform using the SDK, the parameters and settings you enter for the tool are treated as inputs and are accepted by their own input ports.

See also: input, node, SDK, tool, workflow editor

J

Job

The execution of an app is described in terms of its jobs. On the **Task Stats** view, jobs are colored green if they executed successfully, red if they failed, yellow if they were aborted, and blue if they are still in progress.

Tip: To access your tasks, first log into your account. Then, click on the Projects tab. Select the appropriate project to access its Project Dashboard. On the top right corner, you will see a row of tabs. Click on the Tasks tab. Here you can find more information on each executed task as well as each draft task.

See also: app, projectproject dashboard, tool, workflow

M

Main Dashboard

The Main Dashboard is the landing page when you log into the Platform. On the top navigation bar, you can access **Projects**, **Data**, and **Apps**. The **Projects** panel gives a preview of of recent **Projects**. The **Files** panel displays your files. The **Tasks** panel displays a preview of recent tasks.

See also: projectpublic appstask, tool, tool editorworkflow

Manifest

When uploading files to the platform via the command line uploader, a manifest file can be used to [upload multiple files and set the accompanying metadata](doc:set-metadata-using-the-command-line-uploader/).

N

Node

Nodes are the graphical representation of a workflow's building blocks in the Workflow Editor. They represent inputs, outputs, and the tools used to build the workflow.

Tip: Hover over a node in the Workflow Editor to display the descriptions for all possible connections that node can make via input and output ports.

See also: input, input and output ports, tool, workflow, workflow editor

O

P

Permissions

Permissions are assigned to all collaborators in a given project. Permissions include: read, write, copy, execute, and admin. Each of these permissions is mutually exclusive. For example, project members with copy permissions don't need to have execute or write permission.

Tip: You can view project members' permissions in the Project Members panel of the Project Dashboard.

See also: admin permissions, copy permissions, execute permissions, project, project dashboard, project member, read permissions, write permissions

Project

Projects are the core building blocks of the Platform. Each project corresponds to a distinct scientific investigation, serving as a container for its data, analysis tools, results, and team of collaborators. However, multiple workflow executions can be carried out within a project.

See also: project memberworkflow

Project Dashboard

The Project Dashboard is the landing page for a project. Each project has its own dashboard which displays information about the data and workflows within the project. The left navigation panel is an editable project description which you and your collaborators can use to write notes about your project. The project dashboard also includes a Project Member panel and a Task panel, which displays a list of recent tasks. Tabs on the top right for **Files**, **Interactive Analysis**, **Tasks**, **Settings**, and **Notes** give a more detailed view of each feature.

See also: app, projectproject member, task

Project Files

Project Files is a file repository within a project. These files can be viewed, copied, and edited by the project administrator and by project members with copy permissions.

Tip: <div style"margin-left:1em;">

  1. You can view your project permissions in the Project Members panel of the Project Dashboard.
  2. You can copy reference genomes and annotation files from Public Reference Files to your Project Files.

See also: files, project, project dashboard, project member, public reference files

Project Member

Project members are your collaborators on a given project. If you are a project administrator, you can add new collaborators as well as adjust the permissions level of each collaborator. Permissions include: read, write, copy, execute, and admin privileges.

Tip: You can view your collaborators on the Project Members tab of the Project Dashboard.

See also: project, project dashboard

Project short name

Projects are identified by their short names when using the API. A project short name is derived from the name you gave the project when you created it, by:
  • Omitting characters that are not letters or numbers
  • Replacing spaces with hyphens
  • Adding **_1** to any name that is already assigned to one of your projects.

Tip: You can, optionally, override the generated short name to one of your choice when you create a project. To create your own project short name, click the pencil icon on the Create a project pop-out window when you first make the project.

See also: project, project memberworkflow

Public Apps

Public apps are workflows and tools maintained by the Seven Bridges bioinformatics team to represent the latest versions. There are about 150 publicly available tools and workflows.

See also: app, tool, tool editor, workflow, workflow editor

Public Reference Files

Public Reference Files is a repository on the Seven Bridges Platform which contains files that can be used as references, annotation files, and sample data in your analysis. Many bioinformatics tools and workflows require reference and annotation files to work properly. These files are maintained by the Seven Bridges bioinformatics team. These files can be copied to **Project Files** for use in analyses.

Tip: Access this repository by clicking on Data on the navigation bar. Select Public Reference Files from the drop-down menu.

See also: file, project files

R

Read permissions

Read permissions allow users to view file names, metadata, and workflows. They cannot view file contents.

Tip: <div style"margin-left:1em;">

  1. You can view project members' permissions in the Project Members panel of the Project Dashboard.
  2. If you have admin privileges, you can set Read permissions by unchecking all other permissions.

See also: admin permissions, copy permissions, execute permissions, permissions, project, project dashboard, project member, write permissions

S

SDK

The SDK version 2.0 is a toolkit developed by Seven Bridges for installing tools on the Platform. It has two components. The first is the SDK Command Line Interface (CLI), which allows you to install a tool in a Docker container and upload the image to the Platform image registry. The second is the tool editor, which allows you to describe the tool's interface so that it can be run on the Platform.

See also: Docker, tool, tool editor

Seven Bridges Image Registry

The Seven Bridges image registry is a secure storage facility in the same data center as the Seven Bridges Platform compute nodes. It is used to store Docker images containing tools. Keeping your images here rather than in Docker Hub maximizes the efficiency of the tools' setup and runtime when used on the Platform.

See also: Docker, tool, tool editor

Smart Connectors

Smart connectors are graphical representations of the connections between tools in a workflow, through which data flows. They are shown as pipes on the Workflow Editor.

Tip:

  1. Select input/output ports on a node to automatically highlight all possible connections. When you click an output port of a tool, the Workflow Editor will indicate all the input ports of other tools that are compatible with it, by highlighting them in green.
    • For example If your tool outputs FASTQ files, all input ports of other tools on the canvas that accept FASTQs as input will be highlighted.
  2. To undo a connection, hover over the smart connector and scissors will appear, denoting this connection can be severed.

See also: input and output ports, node, tool, workflow

T

Task

A task is a single execution of a tool or a workflow in a project.

Tip: To access your tasks, first log into your account. Then, click on the Projects tab. Select the appropriate project to access its Project Dashboard. On the top right corner, you will see a row of tabs. Click on the Tasks tab. Here you can find more information on each executed task as well as each draft task.

See also: job, projectproject dashboard, [task logs](#section--task logs-), tool, workflow

Task logs

Task logs are produced for every job in the task. They include .log files, std.err files, and std.out files. These are useful when troubleshooting failed tasks.

Tip: To access your task logs, first log into your account. Then, click on the Projects tab. Select the appropriate project to access its Project Dashboard. On the top right corner, you will see a row of tabs. Click on the Tasks tab. Here you can find more information on each executed task as well as each draft task.

See also: job, projectproject dashboard, task, tool, workflow

Task Stats

[Task statistics](doc:view-task-stats) are available for every task on the Platform, which can be useful when optimizing a task or debugging one that has failed.

See also: job, projectproject dashboard, task, tool, workflow

Tool

Tools are programs for processing data on the Platform. Tools can be run alone or as part of a workflow. They are graphically represented in the visual interface as nodes.

Tip: Many tools are maintained by the Seven Bridges bioinformatics team on the Platform as public apps. If you choose to use your own tools, you can import them using the SDK.

See also: node, public apps, SDK, tool editor, workflow

Tool Editor

The Tool Editor is a graphical workspace which allows you to describe a tool's interface, including details of the tool's input and output ports, its command options, and the CPU and memory resources it requires.

Tip:

  1. Once you have filled in a tool's details using the Tool Editor, you can download the JSON file that is the tool's Common Workflow Language (CWL) description.
    • Click on Settings in the Tool Editor then select Tool JSON to see the CWL description.
  2. The Tool Editor outputs a Common Workflow Language (CWL) description of the tool.

See also: input and output ports, tool, workflow

U

User permissions

[User permissions](doc:set-permissions) are set by the project administrator as a way to define which actions each of the collaborators is allowed to perform.

See also: job, projectproject dashboard

V

VCF Benchmarking

The [VCF Benchmarking project](doc:doc:vcf-benchmarking), available as a public project on the Seven Bridges Platform, contains resources which can be used to benchmark a set of variant calls in your VCF file and interactively explore the results from a workflow execution (a "task").

W

Workflow

Workflows are chains of interconnected tools. They are fully modifiable using the workflow editor and can be run as is or added to a project.

Tip: Many workflows are maintained by the Seven Bridges bioinformatics team on the Platform as public apps.

See also: projectpublic apps, tool, workflow editor

Workflow Editor

The Workflow Editor is a graphical workspace in which you can build a workflow from scratch or modify an existing workflow. You can change the ways tools are connected within a workflow and modify the way they run by setting their parameters.

See also: toolworkflow

Write permissions

Write permissions allow users to add, modify, and remove files and workflows in a project.. Collaborators with write permissions do not automatically have execute, write, or admin privileges.

Tip: You can view project members' permissions in the Project Members panel of the Project Dashboard.

See also: admin permissions,copy permissions, execute permissions, permissions, project, project dashboard, project member, read permissions