Code Ocean Computational Lab Release 2.0 adds Visual Pipeline Editor, Remote Access API, Visual Studio Code, alongside workflow improvements and performance enhancements
Code Ocean, the developer of a first-of-its-kind, computational-research laboratory cloud platform for scientific collaboration and discovery, announced Release 2.0 of the Code Ocean Computational Lab, making it the first platform to incorporate both workflow pipelines as well as data science exploratory work targeted for the coding scientist.
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Code Ocean is at the forefront of empowering computational scientists, across disciplines, to focus on science in a digital laboratory. The Code Ocean Computational Lab provides a consistent and secure environment to automate research in the cloud and guarantee fully reproducible research across scientific disciplines. With Release 2.0, the company provides significant new technology additions to the Code Ocean Computational Lab. These include automating the creation of workflow pipelines through a new graphical UI that removes the need for manual Nextflow scripting and a complete automation API for the Code Ocean Computational Lab. The new release also includes support for the open source variant of the popular coding environment, VS Code (Code Server), and adds new features that empower scientists to innovate faster with confidence.
With Release 2.0, computational scientists create, organize and share computational research in a streamlined and automated lab. By removing overhead tasks and simplifying collaboration, computational scientists can focus on science. With strong adoption in bio-pharma, the Code Ocean digital lab has proven its value in accelerating science and reducing the cost of research.
Compute Capsule Pipelines:
Compute Capsules, Code Ocean’s new container technology for computational science, can now be combined in a sequence of Capsules to create custom analytic pipelines. Pipelines can be assembled with a graphical interface that automates the creation of pipelines or, optionally, scripted directly in Nextflow. Scientists can easily create customized workflows from component Capsules and take advantage of different Compute Capsules to build a full end-to-end analytic process. A Capsule pipeline can be created that is independent of language so R, Python, MATLAB, or one of many other languages can be easily combined. Scientists can work in their language of choice and share Capsules with colleagues working in any other environment. The pipeline will automatically scale computational resources with Nextflow on AWS Batch to optimize processing time and deliver intermediate and end results for full pipeline visibility. The generated Nextflow pipelines can be exported and be used outside of the Code Ocean platform so there is no “lock-in,” which is one of the core fundamental product concepts of Code Ocean.
Automation API:
Code Ocean APIs provide access to both data and computational capabilities of the Code Ocean Computational Lab. Developers can leverage the API for automation of repetitive tasks, such as data upload and management, and enable integration of computational workflows into a variety of data, analytics, or production systems. Electronic Notebook (ELN) and Laboratory Information Management (LIM) systems can readily exchange lab data or capture real time data for immediate processing through a Code Ocean Capsule. The Code Ocean API simplifies the link between analytical tools built by computational scientists and physical laboratories where wet lab scientists run experiments and convert data to answers in real time. New analytical science models can be made available to the lab instantly and results generated in the lab immediately leading to faster science and discovery.
New Visual Studio Code Cloud Workstation:
With this release, data scientists and developers can now develop, test, and run their code in the widely popular VS Code (Code Server) environment for their favorite programming language. Complex programs can now be developed within a browser in an efficient and familiar environment. Code Ocean’s unique strength is language independence. Scientists choose their preferred programming language and the automation features of the Code Ocean lab make it simple for collaborators to build complex analysis pipelines.
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New Code Ocean User Interface and Management Features:
The operation of the digital lab has been enhanced to free IT departments from simple management tasks and instead focus on data architecture, building advanced coding environments, and managing the cost of an increasing volume of computations. New features, including a re-designed development interface, have been added across data, Capsule, and account management that improve usability and improve productivity.
- Data management adds support for linking to an external AWS S3 folder within the S3 bucket and new options for sharing, downloading, and archiving datasets
- Project management adds improved filtering for searching and viewing experimental runs across the complete historical timeline of code, data, environment and results
- Compute Capsule versioning using Bitbucket
- Account management expands support for securely managing users’ secrets, credentials, and access tokens
- Cloud Workstation adds new toolbars for data capture and management
- Cost management to monitor and analyze the usage of cloud resources across users and computing resources
Code Ocean’s Computational Lab is available to researchers and companies in two forms: the Computational Lab designed for enterprise and the free Open Science Workbench for researchers and authors in science journals. With advanced features for data storage, analysis pipelines, and API connections to extend the platform, the Code Ocean Computational Lab is a secure virtual lab environment that is deployed with automated access to the customer’s private cloud. Code Ocean’s customers have deployed the lab in both secure deployments with protected patient data and laboratory deployments for development and computational experiments. Code Ocean’s digital lab is also available as a free Open Science Workbench for any scientific developer and authors publishing through Nature, IEEE, Elsevier, and others. With more than 2,500 public research Capsules, the Open Source Library is the only Open Science site with open source code immediately available to run in the cloud from the Open Science Workbench. Code Ocean’s Open Science Library is the new benchmark in Open Science.
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