The Seven Bridges Knowledge Center

The Seven Bridges Platform is a simple solution for doing bioinformatics at industrial scale. But sometimes, everyone needs a little help.

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Creating a bulletproof workflow

Marko Marinkovic · about an hour ago

Many bioinformaticians will have experienced the frustration of inexplicably failed analyses, incorrect outputs, or inconsistent results. When dealing with complex tools and gigabytes or even terabytes of data, it is particularly important to minimize the potential for human error in your analyses. ...

    Release note 2.10.17

    Emile Young · 17 days ago

    Data Browser: Copy all files

    Choose to copy files from a specific File node or from all File nodes on the Data Browser canvas. Learn more about this feature.

    sevenbridges-python 0.7.0

    We've released a new version of the Python bindings for our API, [sevenbridg...

      Release note 02.03.17

      Emile Young · 24 days ago

      Data Browser: Copy all files

      Choose to copy files from a specific File node or from all File nodes on the Data Browser canvas. Learn more about this feature.

        Making efficient use of compute resources

        Andrea Szollossi · about a month ago

        The non-trivial matter of optimising compute resources available for your analysis is brought into the spotlight. We discuss when you might benefit from optimising the compute resources available for your analysis as well as how you can achieve this on the Seven Bridges Platform. Examples of effecti...

          Release note 12.19.16

          Emile Young · 2 months ago

          Seven Bridges Sonar

          Seven Bridges Sonar is a novel platform which allows users to rapidly explore and answer questions spanning genomic and phenomic dimensions and learn from data as it accumulates. On Monday, Dec. 19, we are releasing the Advanced Access (AA) version of Sonar. This is a mix of f...

            Release note 12.12.16

            Emile Young · 2 months ago

            Export and import manifest files

            Take advantage of new options, Export metadata manifest and Import metadata manifest, from the drop-down menu of the Files tab within a project, as shown below.

              Release note 11.28.16

              Emile Young · 3 months ago

              JavaScript cookbook

              Check out our new JavaScript cookbook, which provides examples of expressions that are entered in the Tool Editor when wrapping a tool for use on the Platform.

                Release note 11.21.16

                Emile Young · 3 months ago

                Improve display of user-defined reports

                We’ve improved the display of base64html files. To access an expanded view of the report, select the file from the Files tab in your project dashboard. Then, click Expand report to view the base64html file fullscreen in a new tab.

                Developer Dashb...

                  Developing tools on the Seven Bridges Platform using Docker automated build

                  Marko Marinkovic · 3 months ago

                  This blog post will introduce a solution to enable rapid, iterative development of tools on the Seven Bridges Platform. We will use Dockerfiles – files containing instructions on building a Docker image – and Docker Hub's automated build feature. In short, Docker automated build will use an associat...

                    Did you know: define metadata for your data

                    Emile Young · 3 months ago

                    You can define any metadata fields you like for your Platform files via the command-line uploader or the API.

                      Release note 11.14.16

                      Emile Young · 3 months ago

                      Group parameter settings

                      View parameter settings grouped by the apps they belong to on task-related pages, such as the Draft Task page and Task page. This functionality allows you to toggle between viewing:

                      • all parameters for all apps within your workflow
                      • editable parameters
                      • only the ...

                        Did you know: Docker for Windows

                        Emile Young · 3 months ago

                        The Seven Bridges SDK now supports Windows in addition to Linux and OS X. Learn more about installing Docker on Windows.

                          Release note 11.07.16

                          Emile Young · 3 months ago

                          Documentation update: Tool tips and tricks

                          Check out our new pages on tips and tricks for tools. These pages go over making files available in your tool’s working directory, [setting the default value for an...

                            Did you know: Contextual help

                            Emile Young · 4 months ago

                            You can click the question mark icon located at the top of each page of the Platform's visual interface to get contextual documentation help. For instance, you can see the following on the Files tab of a project:

                              Release note 10.24.16

                              Emile Young · 4 months ago

                              sevenbridges-python error handling

                              sevenbridges-python 0.6.0 adds error handling libraries to overcome rate limits and platform issues. Users can also add detailed error logging.

                              Working with Volumes

                              We've updated our tutorials on working with volumes for both S3 and Google Cloud Storage b...

                                Release note 10.17.16

                                Emile Young · 4 months ago

                                Create and use folders via the API

                                You can organize your project files within folders via specific API requests. The Folders functionality is an advanced access feature, which means specific feature details are subject to change. Each project is a root folder containing all your project files. Cr...

                                  Release note 10.10.16

                                  Emile Young · 4 months ago

                                  Visual interface improvements for adding files and apps

                                  We've updated the visual interface of the Platform to make adding files and apps intuitive and convenient. For instance, you can browse and add apps from the Seven Bridges Public Apps repository, all without leaving your project.

                                    Release note 10.03.16

                                    Emile Young · 4 months ago

                                    job.tree.log for job executions

                                    After each job execution, the Platform will generate a job.tree.log file. This file contains the structure of the working directory and can be useful in the debugging process. Learn more from our documentation...

                                      Did you know: Suggested files

                                      Emile Young · 5 months ago

                                      Our bioinformaticians have curated a set of recommended input files for each public workflow to simplify and optimize the process of selecting input files when setting up an analysis.


                                        Release note 09.27.16

                                        Emile Young · 5 months ago

                                        Graph-based Whole Genome Sequencing Analysis app (Priority access)

                                        We're releasing a Whole Genome Sequencing Analysis app based on our graph genome technology. This highly efficient app calls accu...

                                          Did you know: View and save all task logs

                                          Emile Young · 5 months ago

                                          You can save and view all task logs produced during a task. These logs include the explicit commands used to execute your task (cmd.log) and details of the execution, including input and output data, metadata and resources used (job.json). The Platform saves these logs by default for tasks init...

                                            Release note 09.05.16

                                            Emile Young · 5 months ago

                                            This week, we have a few exciting features to announce! Please read on for more details. As always, don't hesitate to reach out to our team if you have any feedback.

                                            Tag files via the API

                                            Previously, we introduced file tagging on the visual interface to facilitate finding and organizing your dat...

                                              Release note 08.22.16

                                              Emile Young · 6 months ago

                                              This week, we have a few exciting features to announce! Please read on for more details. As always, don't hesitate to reach out to our team if you have any feedback.

                                              Set metadata using a manifest file

                                              Adding metadata to files just got easier. You can now import tabular m...

                                                Release note 08.08.16

                                                Emile Young · 6 months ago

                                                Updated Genome Browser

                                                The genome browser now supports visualization of BAM files aligned with GRCh38 and hg38. Learn more from our documentation.

                                                  Release note 08.01.16

                                                  Emile Young · 7 months ago

                                                  Better Feedback Form

                                                  We love hearing how researchers use our Platform, and ways that we can make it better.

                                                  To make it easier for you, we've made some improvements to our feedback collection feature. Enhancements are subtle, but it is now easier for your to shape your feedback as idea, problem ...

                                                    Recent improvements to the Seven Bridges Platform

                                                    Emile Young · 7 months ago

                                                    Over the last several weeks we’ve added a number of features to make it easier for you to use the Seven Bridges Platform to learn more from your data even more efficiently. We are shifting from announcing changes on a per-version basis to a calendar-based cycle which more accurately reflects our cu...

                                                      What happens when I run a task?

                                                      Aleksandar Gazibara · 7 months ago

                                                      Each time you run a tool or a workflow on the Seven Bridges Platform, you create a task. The task goes through several different phases before it is finally completed. A change in its status, displayed in the upper left corner of the task page, marks off each phase, as shown below.

                                                        Customizing your tasks on the Seven Bridges Platform

                                                        Marko Marinkovic · 7 months ago

                                                        This blog post will provide an overview of how hints can be used to customize tasks on the Seven Bridges Platform. In the context of the Platform, "hints" are parameters that are entered in the visual interface and allow you to configure or override some of the predefined ways in which apps and task...

                                                          Announcing the release of Seven Bridges' API clients in R and Python

                                                          Kate Hodesdon · 9 months ago

                                                          The Seven Bridges Application Programming Interface (API) has allowed our users to automate, extend, and customize their analysis pipelines. We currently have more than 50 officially supported calls and some additional calls in the Advanced Access Program. We use a REST architecture with calls detai...

                                                            Release notes 3.29

                                                            Kate Hodesdon · 10 months ago

                                                            This week, we updated the way that files are validated when setting up a task on the Platform. From now, there will be better, more informative error messages when you set an input that requires a secondary (index) file that is not found in the project.

                                                              Release notes 3.28

                                                              Kate Hodesdon · 10 months ago

                                                              This week, we released a new Python library with bindings for the API. See the external documentation hosted on readthedocs for details.

                                                                Release notes 3.27

                                                                Kate Hodesdon · 10 months ago

                                                                This week, we have released support to modify the way that tasks handle batching via the API.

                                                                We've also released functionality to configure the instance types used in a task.

                                                                To support the documentation on the instances used in tasks, we released details of the...

                                                                  The new normal: portable workflows

                                                                  Kate Hodesdon · 10 months ago

                                                                  Since 2014, researchers around the world, including engineers and scientists at Seven Bridges, have been developing the Common Workflow Language (CWL) specification. The ambitious goal of this project is to enable portable, reproducible and scalable biomedical data analysi...

                                                                    Release notes 3.25

                                                                    Kate Hodesdon · 10 months ago

                                                                    This week we enabled tasks to be run in batches, improving the way that the Platform performs at scale. We also released a new API that lets you run analyses using files housed in your own AWS or Google cloud storage, without the need to import them to the Platform.

                                                                      Release notes 3.24

                                                                      Kate Hodesdon · 11 months ago

                                                                      This week we deployed two major additions to the API and a nice improvement to the notes feature. Details below.

                                                                      We've also added a tutorials section to the documenta...

                                                                        Release notes 3.23

                                                                        Kate Hodesdon · 11 months ago

                                                                        This week saw ongoing updates, but no significant new features deployed to the Seven Bridges Platform.

                                                                          Release notes 3.22

                                                                          Kate Hodesdon · 11 months ago

                                                                          Improved task stats

                                                                          This week we improved the way that statistics and logs for tasks (app executions) are presented on the Platform.

                                                                          You can now see a timeline showing the jobs run for each task, and explore their logs. See the documentation here...

                                                                            Release notes 3.21

                                                                            Kate Hodesdon · 11 months ago

                                                                            This week we deployed some updates to the Seven Bridges API.

                                                                            The public API v2 now supports file filtering.
                                                                            This means that you can request information about files in a specified project, with further specific names, metadata, or which were produced by a...

                                                                              Release notes 3.20

                                                                              Kate Hodesdon · 12 months ago

                                                                              This week saw several new features go to the Seven Bridges Platform.

                                                                                Projects on the Seven Bridges Platform: some differences for AWS and Google Cloud users

                                                                                Seven Bridges · about a year ago

                                                                                We recently deployed the Seven Bridges Platform on Google’s cloud infrastructure. This means that we can offer new Seven Bridges users a choice of underlying platform service provider: either Amazon Web Services (AWS), who have powered our Platform to date, or G...