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

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.

Scientists Press AI Researchers for Transparency | Science | TechNewsWorld
02/01/2021
Scientists Press AI Researchers for Transparency

Scientists Press AI Researchers for Transparency | Science | TechNewsWorld

An international group of scientists is demanding scientific journals demand more transparency from researchers in computer-related areas when accepting their reports for publication. They also want computational researchers to include information about their code, models and computational environme...

Explore & Run #COVID-19 #computational research with #DeepLearning code #ComputationalScience #Bioinformatics #Biotechno...
01/26/2021

Explore & Run #COVID-19 #computational research with #DeepLearning code #ComputationalScience #Bioinformatics #Biotechnology https://buff.ly/2Yarojv

Explore & Run #COVID-19 #computational research with #DeepLearning code #ComputationalScience #Bioinformatics #Biotechnology https://buff.ly/2Yarojv

On-demand webinar:  Learn how AACR and researchers use @codeoceanhq to capture a self-contained executable compute capsu...
01/25/2021
AACR Journals – Code Ocean: A Tool to Support the Delivery of Reproducible Analysis - Code Ocean

On-demand webinar: Learn how AACR and researchers use @codeoceanhq to capture a self-contained executable compute capsule which packages: code, data, analyze results, and the run environment.

This webinar features Benjamin Haibe-Kains of University of Toronto discussing how Code Ocean allows for the inclusion of an executable instance of the code for peer review and publication Overview The complexity of cancer research data is causing researchers to rely on increasingly sophisticated an...

@SimonAdar > Together, Code Ocean and Lumin offers a complete computational analysis solution for data-driven drug disco...
01/19/2021
Lumin Bioinformatics Software Featuring Code Ocean

@SimonAdar > Together, Code Ocean and Lumin offers a complete computational analysis solution for data-driven drug discovery https://buff.ly/3p4V3Xe #ChampionsOncology #LuminBioinformatics #Oncology #BioInformatics #Biotechnology

Lumin features expanded code ocean functionality for centralizing, storing, and organizing code and data while leveraging single-tenant hosting.

01/19/2021
Champions Oncology Announces Partnership with Code Ocean to Expand the Functionality of Lumin Bioinformatics - Code Ocean

@SimonAdar > We’re excited to partner with Champions Oncology to bring computational research-ready solutions directly to Lumin Bioinformatics customers" https://buff.ly/39Lb6Tt #ChampionsOncology #LuminBioinformatics

HACKENSACK, NJ – January 19, 2021 9:00AM – Champions Oncology, Inc. (Nasdaq: CSBR), a leading global oncology technology company that is transforming drug discovery and development through data-driven research strategies, announced today a partnership with Code Ocean to expand the functionality ...

Champions Oncology announces partnership with Code Ocean to expand the functionality of its SaaS program, Lumin Bioinfor...
01/19/2021

Champions Oncology announces partnership with Code Ocean to expand the functionality of its SaaS program, Lumin Bioinformatics. https://buff.ly/3qziUhX #BioInformatics #Biotechnology Code Ocean #ChampionsOncology Champions Oncology

Champions Oncology announces partnership with Code Ocean to expand the functionality of its SaaS program, Lumin Bioinformatics. https://buff.ly/3qziUhX #BioInformatics #Biotechnology Code Ocean #ChampionsOncology Champions Oncology

“If research includes the use of software code, statistical analysis or algorithms then we also recommend that authors u...
01/17/2021
Archaeology International

“If research includes the use of software code, statistical analysis or algorithms then we also recommend that authors upload the code into Code Ocean" #computationalresearch @CodeOceanHQ https://bit.ly/3qvcFM8

ISSN: 2048-4194 Contact the journal All general enquiries should be sent to the Editor-in-Chief Dr Alice Stevenson [email protected] Read now The UCL Institute of Archaeology is the largest centre for research and teaching in the fields of archaeology, cultural heritage, conservation and mus...

Code Ocean's cover photo
12/20/2020

Code Ocean's cover photo

Code Ocean's cover photo
05/28/2019

Code Ocean's cover photo

One computer scientist explores how creating documentation and a demo for code increases its accessibility. http://bit.l...
03/28/2018

One computer scientist explores how creating documentation and a demo for code increases its accessibility. http://bit.ly/2CA1eKL

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Good idea! We will be here a lot!