Code Ocean

Code Ocean Where great computational research is faster, more collaborative, achieving higher quality discoveries. Code Ocean is the best way to standardize research workflow, plus track and reproduce all computations and discoveries with:
-Out-of-the-box popular computational tools
-Easy access to any computing resource and data storage
-Integrated collaboration and access control
-Centralized repository to keep projects and results organized
(3)

Operating as usual

Last chance to register! Join us tomorrow, June 23rd at 11 am EST to learn how to improve the speed, efficiency, and res...
06/22/2021
Webinar: How to Speed Up Cancer Genomics with Multi-Omics Analysis

Last chance to register! Join us tomorrow, June 23rd at 11 am EST to learn how to improve the speed, efficiency, and results of cancer genomics. We’re looking forward to a great discussion with industry experts Benjamin Haibe-Kains, Senior Scientist at the Princess Margaret Cancer Centre and Simon Adar, CEO of Code Ocean.

You won’t want to miss this webinar!

https://hubs.ly/H0PKrpr0
#genomics #multiomics #bioinformatics #computationalbiology

How can researchers improve the speed, efficiency, and results of cancer genomics? In this webinar, industry experts share their insight.

Just one more week until our webinar on streamlining cancer genomics multi-omics analysis on June 23rd. Join us for a li...
06/16/2021
Webinar: How to Speed Up Cancer Genomics with Multi-Omics Analysis

Just one more week until our webinar on streamlining cancer genomics multi-omics analysis on June 23rd. Join us for a lively discussion on preparing curated datasets and streamlining analysis. Plus, see the suggested structure applied to a multi-omics analysis in action!

Register now: https://hubs.ly/H0PKrp40
#genomics #multiomics #bioinformatics #computationalbiology

How can researchers improve the speed, efficiency, and results of cancer genomics? In this webinar, industry experts share their insight.

Cancer genomics research is exploding with multi-omics and multimodal data, but this brings new challenges. Learn how to...
06/08/2021
Webinar: How to Speed Up Cancer Genomics with Multi-Omics Analysis

Cancer genomics research is exploding with multi-omics and multimodal data, but this brings new challenges. Learn how to streamline research (and improve speed, results, and ROI) in this informative webinar on June 23rd.

In this webinar, industry experts Benjamin Haibe-Kains, Senior Scientist at the Princess Margaret Cancer Centre and Simon Adar, CEO of Code Ocean, will share their insight based on a suggested framework for multimodal pharmacogenomics data analysis. You won’t want to miss this event!

Save your seat: https://hubs.ly/H0PKr9v0
#genomics #multiomics #computationalbiology #bioinformatics

How can researchers improve the speed, efficiency, and results of cancer genomics? In this webinar, industry experts share their insight.

Do you find it challenging to analyze multi-omics data and make the most out of it? Find out how to drastically improve ...
06/03/2021
Webinar: How to Speed Up Cancer Genomics with Multi-Omics Analysis

Do you find it challenging to analyze multi-omics data and make the most out of it? Find out how to drastically improve the speed, efficiency, and results in this can't-miss webinar.

Join industry experts Benjamin Haibe-Kains, Senior Scientist at the Princess Margaret Cancer Centre and Simon Adar, Code Ocean CEO as they discuss how to curate and prepare pharmacogenomics datasets, streamline and democratize gene analysis, and more.

Save your seat: https://hubs.ly/H0PwCRZ0

#genomics #multiomics #computationalbiology #bioinformatics

How can researchers improve the speed, efficiency, and results of cancer genomics? In this webinar, industry experts share their insight.

Open #ComputeCapsule --> "Combo Synergy of Two Drugs Capsule" - Thanks to the Authors!  https://buff.ly/3vCYWFX @CodeOce...
06/02/2021

Open #ComputeCapsule --> "Combo Synergy of Two Drugs Capsule" - Thanks to the Authors! https://buff.ly/3vCYWFX @CodeOceanHQ #ComputationalBiology #Bioinformatics #Biotechnology #Sequencing

Open #ComputeCapsule --> "Combo Synergy of Two Drugs Capsule" - Thanks to the Authors! https://buff.ly/3vCYWFX @CodeOceanHQ #ComputationalBiology #Bioinformatics #Biotechnology #Sequencing

Cancer genomics research is experiencing exponential growth of multi-omics data. The problem? This paradigm shift still ...
05/27/2021
Webinar: How to Speed Up Cancer Genomics with Multi-Omics Analysis

Cancer genomics research is experiencing exponential growth of multi-omics data. The problem? This paradigm shift still leaves researchers with slow analysis, manual curation, and lowering ROI on discovery.

So how can researchers improve the speed, efficiency, and results of cancer genomics analysis? Join our upcoming webinar for a lively discussion and demo!

We’ll host industry expert Benjamin Haibe-Kains, Senior Scientist at the Princess Margaret Cancer Centre to discuss how to curate datasets, streamline collaboration, and democratize gene analysis.

Register now: https://hubs.ly/H0P7p8p0
#cancergenomics #multiomicanalysis #computationalbiology #bioinformatics #multiomics

How can researchers improve the speed, efficiency, and results of cancer genomics? In this webinar, industry experts share their insight.

What is a #ComputeCapsule and how does it help researchers collaborate @CodeOceanHQ #Bioinformatics #ComputationalBiolog...
05/19/2021

What is a #ComputeCapsule and how does it help researchers collaborate @CodeOceanHQ #Bioinformatics #ComputationalBiologist #Research https://buff.ly/3ovXyCd

What is a #ComputeCapsule and how does it help researchers collaborate @CodeOceanHQ #Bioinformatics #ComputationalBiologist #Research https://buff.ly/3ovXyCd

We are excited to announce our $21M in funding to accelerate in biotech. Thanks to our entire community of customers, pu...
05/17/2021

We are excited to announce our $21M in funding to accelerate in biotech. Thanks to our entire community of customers, publishers, and researchers! https://hubs.ly/H0NwlyL0 @CodeOceanHQ #Biotechnology #ComputationalBiology #ComputationalScience #DrugDiscovery

We are excited to announce our $21M in funding to accelerate in biotech. Thanks to our entire community of customers, publishers, and researchers! https://hubs.ly/H0NwlyL0 @CodeOceanHQ #Biotechnology #ComputationalBiology #ComputationalScience #DrugDiscovery

05/12/2021
Last chance to register! Join us tomorrow, May 13th at 11 am EST to learn why high throughput collaboration in computational biology is the future. Bring your toughest questions for industry experts Yair Benita and Simon Adar about building productive te

Last chance to register! Join us tomorrow, May 13th at 11 am EST to learn why high throughput collaboration in computational biology is the future. Bring your toughest questions for industry experts Yair Benita and Simon Adar about building productive teams, troubleshooting code, and expediting time to results.

https://hubs.ly/H0N06KW0

#computationalbiology #reproducibility #computationalresearch #biotech #informatics #bioinformaticssoftware

Open #ComputeCapsule --> "Monet For Analyzing #scRNA-seq" - Thanks to Author!  https://buff.ly/3vSdfpG @CodeOceanHQ #Com...
05/11/2021

Open #ComputeCapsule --> "Monet For Analyzing #scRNA-seq" - Thanks to Author! https://buff.ly/3vSdfpG @CodeOceanHQ #ComputationalBiology #Bioinformatics #Biotechnology #Sequencing

Open #ComputeCapsule --> "Monet For Analyzing #scRNA-seq" - Thanks to Author! https://buff.ly/3vSdfpG @CodeOceanHQ #ComputationalBiology #Bioinformatics #Biotechnology #Sequencing

Open #ComputeCapsule --> "Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences" -...
05/07/2021

Open #ComputeCapsule --> "Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences" - Thanks Authors! @CodeOceanHQ https://buff.ly/2SxJiNw #ComputationalBiology #Bioinformatics #Biotechnology #NextGenerationSequencing

Open #ComputeCapsule --> "Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences" - Thanks Authors! @CodeOceanHQ https://buff.ly/2SxJiNw #ComputationalBiology #Bioinformatics #Biotechnology #NextGenerationSequencing

Just one more week until our webinar on May 13. Find out how and why bioinformaticians and computational biologists have...
05/06/2021
Webinar: Boosting Productivity | Code Ocean

Just one more week until our webinar on May 13. Find out how and why bioinformaticians and computational biologists have begun collaborating to move faster, improve their work quality, and reproduce results more easily.

In this webinar, industry experts Yair Benita and Simon Adar will share real-world use cases that illustrate how high throughput collaboration has enabled the team to reach results faster than ever.

Register now! https://hubs.ly/H0MGh9f0
#computationalbiology #reproducibility #computationalscience #bioinformatics #informaticssoftware

Join us for a webinar and learn a collaborative approach for research productivity to achieve high-performance bioinformatics collaboration with guaranteed code reproducibility.

04/29/2021
Driven by technological advancements, bioinformaticians, computational biologists, scientists, and discovery IT are quickly moving away from the traditional go-it-alone model. Why? High throughput collaboration and teamwork drives results. Join us on May

Driven by technological advancements, bioinformaticians, computational biologists, scientists, and discovery IT are quickly moving away from the traditional go-it-alone model.

Why? High throughput collaboration and teamwork drives results.

Join us on May 13th as we discuss how to build a collaborative team, processes you can leverage tomorrow, out-of-the-box technologies to operationalize research teams, and more.

Save your seat: https://hubs.ly/H0M7xb40

#computationalbiology #reproducibility #computationalscience #bioinformatics #bioinformaticssoftware

Sharing computational analysis. Here's a new blog post "What is a Compute Capsule?"  A standard executable software pack...
04/28/2021
What is a Compute Capsule™? - Code Ocean

Sharing computational analysis. Here's a new blog post "What is a Compute Capsule?" A standard executable software package that makes sharing fast and reproducible. #computationalbiologist #computationalchemist #Bioinformatics #drugdiscovery

At Code Ocean our mission is to empower researchers with easy-to-use computational tools that make their work efficient, reproducible and collaborative and help them achieve faster and higher quality discoveries. Our Compute Capsules™ are what make that mission a reality. Compute Capsules allow co...

High throughput collaboration is fast becoming the new normal in computational biology. Why? Join our upcoming webinar t...
04/21/2021
Webinar: Boosting Productivity | Code Ocean

High throughput collaboration is fast becoming the new normal in computational biology. Why? Join our upcoming webinar to find out!

You’ll hear from industry experts Yair Benita of CytoReason and our Founder and CEO Simon Adar on the proven frameworks, processes, and technology to help you get started with high throughput collaboration. Bring your questions!

Register now: https://hubs.ly/H0LHzcj0

#computationalbiology #reproducibility #computationalscience #bioinformatics #bioinformaticssoftware

Join us for a webinar and learn a collaborative approach for research productivity to achieve high-performance bioinformatics collaboration with guaranteed code reproducibility.

“We partner with @CodeOceanHQ Ocean and protocols.io to support the creation of research and the dissemination of code, ...
03/11/2021
An interview with EBSCO’s Tamir Borensztajn

“We partner with @CodeOceanHQ Ocean and protocols.io to support the creation of research and the dissemination of code, data and methods. ” #reproducibility #computationalresearch #computationalscience

In February 2021, EBSCO became a sustaining contributor of DOAJ. I sat down with EBSCO’s Tamir Borensztajn, Vice President of Saas Strategy, to chat about EBSCO’s role as a discovery se…

Y-LineageTracker is an open-source and user-friendly tool to analyze Y-DNA from NGS data at both Y-SNP and Y-STR level. ...
03/11/2021

Y-LineageTracker is an open-source and user-friendly tool to analyze Y-DNA from NGS data at both Y-SNP and Y-STR level. Code available @CodeOceanHQ #ComputeCapsule https://buff.ly/2N3LGsS #bioinformatics #sequencing https://buff.ly/3t5xKxV

Y-LineageTracker is an open-source and user-friendly tool to analyze Y-DNA from NGS data at both Y-SNP and Y-STR level. Code available @CodeOceanHQ #ComputeCapsule https://buff.ly/2N3LGsS #bioinformatics #sequencing https://buff.ly/3t5xKxV

So easy!
03/10/2021

So easy!

New in GigaByte: SMARTdenovo, a de novo assembler using long noisy reads. Which incidentally is our second software paper with a Code Ocean compute capsule to test it out.

https://doi.org/10.46471/gigabyte.15

Apply for BioHacks 2021.  Deadline today.
03/10/2021
BioHacks 2021: Technology in a Pandemic World - Code Ocean

Apply for BioHacks 2021. Deadline today.

The University of Toronto’s Bioinformatics and Computational Biology Student’s Union Hackathon BioHacks 2021 is a free, virtual bioinformatics hackathon aiming to tackle epidemic health issues raised by COVID-19. Come compete in the upcoming hackathon to create new projects or run analyses on an...

Similarity-driven multi-view embeddings from high-dimensional biomedical data#SiMLR @nature https://buff.ly/3rxTWAq  All...
03/10/2021

Similarity-driven multi-view embeddings from high-dimensional biomedical data
#SiMLR @nature https://buff.ly/3rxTWAq All visualized plots in the main manuscript are generated from our code #ComputeCapsule #sequencing #bioinformatics #Biotechnology https://buff.ly/3t6WbLA

Similarity-driven multi-view embeddings from high-dimensional biomedical data
#SiMLR @nature https://buff.ly/3rxTWAq All visualized plots in the main manuscript are generated from our code #ComputeCapsule #sequencing #bioinformatics #Biotechnology https://buff.ly/3t6WbLA

Using Code Ocean for sharing reproducible research | The Princeton Research Software Engineering Group Blog #computation...
03/10/2021
Using Codeocean for sharing reproducible research | The Princeton Research Software Engineering Group Blog

Using Code Ocean for sharing reproducible research | The Princeton Research Software Engineering Group Blog #computationalscience #bioinformatics #biotechnology #computationalresearch

Using Codeocean for sharing reproducible research Posted on March 5, 2021 by Troy Comi As a researcher, inquiries about previously published research probably evoke two feelings: panic-filled regret or calm authority. Often the difference is time; it’s easier to talk about the project you worked o...

03/09/2021

We're excited to be speaking and joining the computational biology community at this Virtual Hackathon! @universitytoronto @thePMCF #computationalbiology https://buff.ly/2OjufoT

Shared #ComputeCapsule > clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from...
03/08/2021
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Shared #ComputeCapsule > clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers @codeocean #geneexpression #computationalbiology #biotechnology #bioninformatics #drugdiscovery

Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be ma...

What Is Open Science? With Code Ocean Compute Capsules make open science research transparent, reusable, and reproducibl...
03/02/2021
What Is Open Science?

What Is Open Science? With Code Ocean Compute Capsules make open science research transparent, reusable, and reproducible #reproducibility @MATLAB @CodeOceanHQ

MATLAB supports Open Science by enabling scientists to write transparent code and share it freely with their communities. Resources include videos, articles, and ideas for Open Science with MATLAB.

@GenomeBiology Genome Biology is partnering with with Code Ocean, with the aim of making the peer review of source code ...
02/23/2021
Promoting reproducibility with Code Ocean

@GenomeBiology Genome Biology is partnering with with Code Ocean, with the aim of making the peer review of source code easier for both reviewers and authors #reproducibility #computationalscience #bioinformatics @CodeOceanHQ

Editorial Open Access Published: 19 February 2021 Promoting reproducibility with Code Ocean Barbara Cheifet1 Genome Biology volume 22, Article number: 65 (2021) Cite this article 198 Accesses 11 Altmetric Metrics details Genome Biology has built a reputation in the community for our strong data depo...

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data > Source code used for da...
02/17/2021
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data > Source code used for data analysis and viz is publicly available @CodeOceanHQ at https://buff.ly/3bgIPon @BMCBiology #biotechnology #RNA

Background The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to nor...

02/04/2021
Scholarly Products

“ tools such as Code Ocean offer independent code validation and sharing platforms” #computationalscience

In addition to peer-review publications, there are many ways you can make sure the product of your scholarly efforts have life beyond the benchtop.

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Good idea! We will be here a lot!