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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

Operating as usual

Biotech is exploding - but why now? According to industry expert Yair Benita:- Disease models: We've progressed to human...
02/21/2022
Why is Biotech Exploding Now?

Biotech is exploding - but why now? According to industry expert Yair Benita:
- Disease models: We've progressed to human data rather than animal models
- Data: We've moved from manually generated data to robotics and then omics profiling, meaning we now work with massive amounts of data
- Technology: Research progressed from studying a single gene to full single cells from a patient
- Analytics: Gone are the days of Excel - computational tools and team analytics are now required to handle all that data.

https://hubs.ly/Q014yC2v0

#biotech #computationalbiology #dataanalysis

Biotech is exploding - but why now? Industry expert Yair Benita shares four factors that impact this uptick:- Disease models: Today, we have progressed to hu...

We often see organizations of all sizes struggling with maintaining #computationalanalysis data, results, and knowledge ...
02/18/2022
9 Challenges Computational Researchers Need to Address in 2022

We often see organizations of all sizes struggling with maintaining #computationalanalysis data, results, and knowledge created by one individual on their computer and transferring it to the organization. When a team member leaves the organization, often their work is lost or extremely difficult to recover or recreate. Keeping aggregated knowledge within the organization is a goal for many computational research teams. How does your team solve this issue?

https://hubs.ly/Q014sypt0

#computationalbiology

Science these days is inseparably linked with computational analysis. All organizations whether small biotechs, large (bio)pharma companies or academic research groups have a computational element to their work that is gaining in importance as automation enables bench scientists to generate ever lar...

Computational projects are designed to help answer a critical scientific question, which means they are complex. Splitti...
02/17/2022
9 Challenges Computational Researchers Need to Address in 2022

Computational projects are designed to help answer a critical scientific question, which means they are complex. Splitting these large and complicated problems into subtasks with different team assignments is a challenge: Teams need to be able to quickly access data, launch the tools they need, and reassemble the different components for a project to see success.

Does your computational team face challenges dividing up projects?

https://hubs.ly/Q014ldq90

#computationalresearch #biotech

Science these days is inseparably linked with computational analysis. All organizations whether small biotechs, large (bio)pharma companies or academic research groups have a computational element to their work that is gaining in importance as automation enables bench scientists to generate ever lar...

The Compute Capsule contains the essential triplet of any #computationalanalysis: the code, the data, and the computing ...
02/16/2022
Code Ocean Compute Capsules Support Reproducibility

The Compute Capsule contains the essential triplet of any #computationalanalysis: the code, the data, and the computing environment in a single executable package. These three components are separated and distinct, but also held together and executable, making it easy to follow best practices in computational research.

Here's how the Compute Capsule supports reproducibility:
- The environment is built with Docker, with pinned versions for reproducibility.
- Code Ocean is built on Git for version control - you can track changes, see commit history, use different branches, and more.
- Build a repository of Capsules and templates to use for other projects and reproduce results with the click of a button.

https://hubs.ly/Q013_qNt0

#computationalresearch #computationalscience #reproducibility

The Compute Capsule contains the essential triplet of any computational analysis: the code, the data, and the computing environment in a single executable pa...

We asked computational researchers about their biggest challenges, and the results really echoed what we are seeing in t...
02/15/2022
Poll: What are your biggest computational research challenges?

We asked computational researchers about their biggest challenges, and the results really echoed what we are seeing in the field:
1. Sharing research with non-coders
2. Full visibility and traceability of a computational project
3. Maintaining computing environment and access to resources

https://hubs.ly/Q013_qNr0

#computationalresearch #computationalbiology

We asked computational researchers about their biggest challenges, and the results really echoed what we are seeing in the field:1. Sharing research with non...

See how Sema4 expedites research with the Code Ocean platform: https://hubs.ly/Q013_mPx0#genomics #compbio #computationa...
02/14/2022
How Sema4 Is Shortening Time to Innovation

See how Sema4 expedites research with the Code Ocean platform: https://hubs.ly/Q013_mPx0

#genomics #compbio #computationalresearch

How Sema4 Is Shortening Time to Innovation by Increasing Productivity Through the Use of Code Ocean Compute Capsules™ Code Ocean client Sema4 collects, aggregates, and analyzes large amounts of complex clinical and genomic data, which presented challenges for the fast-paced, rapidly growing compan...

The explosion of the computational research field has led to challenges with collaboration that can slow discovery. High...
02/11/2022
How Does High Throughput Collaboration Improve Computational Research?

The explosion of the computational research field has led to challenges with collaboration that can slow discovery. High throughput collaboration helps solve these problems, making the research, code, data, environment, and results easy to share and trace. This empowers researchers to do what they do best: make discoveries.

https://hubs.ly/Q013yxgP0

The explosion of the computational research field has led to challenges with collaboration that can slow discovery. High throughput collaboration through Cod...

02/10/2022
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Interesting study from Code Ocean customer CytoReason on how tuMap enables high-resolution quantitative comparison of cancer samples, improving metric generation and evaluation for cancer patients.

https://hubs.ly/Q013yt1f0

Managing teams and projects is a crucial challenge in computational research. With teams of bioinformaticians and resear...
02/09/2022
9 Challenges Computational Researchers Need to Address in 2022

Managing teams and projects is a crucial challenge in computational research. With teams of bioinformaticians and researchers crunching huge, complex multi-omics data sets, the challenge is managing many different skill sets and – in the absence of established best practices – develop a methodology for standardized, consistent data analysis.

How does your team address this challenge?

https://hubs.ly/Q013yvp40

#compbio #computationalscience

Science these days is inseparably linked with computational analysis. All organizations whether small biotechs, large (bio)pharma companies or academic research groups have a computational element to their work that is gaining in importance as automation enables bench scientists to generate ever lar...

We often see teams operating in silos in computational research. Different people have different skills and backgrounds,...
02/08/2022
Challenges with Teamwork in Computational Research

We often see teams operating in silos in computational research. Different people have different skills and backgrounds, use different tools, and may even code in different languages.

- Bioinformatics teams handle data processing and pipeline
- Computational teams work with modeling, analysis, and machine learning
- Experimental teams perform interactive analysis and discovery
- IT handles applications and infrastructure

Effortless collaboration between these groups is difficult, and creates a large ecosystem of languages, tools, packages, and applications to know and leverage.

#computationalresearch #bioinformatics

https://hubs.ly/Q013ytmv0

In computational research groups, we're often seeing teams operating in silos. Different people have different skills, they come from different backgrounds, ...

Effective collaboration in computational research requires that team members can quickly and easily share data, code, co...
02/07/2022

Effective collaboration in computational research requires that team members can quickly and easily share data, code, computing environment, and results - within their team and cross-functionally:
- Bioinformaticians need to give computational biologists easy access to their data pipeline so they can build on their results
- Engineers need to share data and algorithms with bioinformaticians and computational biologists for data preparation and analysis
- Computational biologists need to share data, code, and results with in-house and partner researchers

Traditional tools lack the functionality to enable shareability, leading to a host of issues from delayed progress to security to version control. What shareability challenges do you have at your organization?

#biotech #compbio

Where does communication break down among researchers, and why? 1. They don’t have an easy-to-use, out-of-the-box user e...
02/03/2022
What Gaps Impact Computational Research Reproducibility?

Where does communication break down among researchers, and why?
1. They don’t have an easy-to-use, out-of-the-box user environment
2. They don’t have an easy way to share research that’s reproducible and works every time
3. They lack a common repository where they can share data, analysis, and results

#reproducibility #computationalresearch #bioinformatics

https://hubs.ly/Q013l5ZX0

Where are the gaps impacting reproducibility in computational research? Alicia Liu, Application Scientist at Code Ocean, breaks down common issues into two c...

What are the biggest challenges computational researchers face? Handling DevOps tasks has to be one of them. Researchers...
02/02/2022
9 Challenges Computational Researchers Need to Address in 2022

What are the biggest challenges computational researchers face? Handling DevOps tasks has to be one of them. Researchers aren't IT specialists and shouldn't have to set up security and computing infrastructure.

What are the top challenges you struggle with in computational research?

https://hubs.ly/Q013ld320

#computationalresearch #computationalscience #biopharma #DevOps

Science these days is inseparably linked with computational analysis. All organizations whether small biotechs, large (bio)pharma companies or academic research groups have a computational element to their work that is gaining in importance as automation enables bench scientists to generate ever lar...

#ComputationalBiology is growing at the fastest rate we've ever seen. 1. Next gen sequencing technology is creating expo...
02/01/2022
Key Challenges in the Computational Biology Field

#ComputationalBiology is growing at the fastest rate we've ever seen.
1. Next gen sequencing technology is creating exponentially large amounts of data
2. As a result, analysis is becoming more complicated
3. We now need teams of computational researchers working with biologists to see results and create true progress

#computationalresearch #compbio

https://hubs.ly/Q013b8bD0

Computational biology as a field is growing and changing at a rapid pace, and this brings challenges for research teams. Code Ocean Application Scientist Ali...

What are the top challenges in Computational Research today? I interviewed dozens of researchers last year and found the...
01/12/2022
Challenges in Computational Research - Distilling a Year of Conversations

What are the top challenges in Computational Research today? I interviewed dozens of researchers last year and found these common challenges:

1.The software tools they use don’t work well together. Computational research teams spend ALMOST HALF their time trying to get various software packages and tools to work together.

2. DevOps tasks are the bane of every computational scientist’s existence. Setting up cloud infrastructure and security or configuring and accessing data are not their core competencies.

3. The larger the organization, the more siloed the information becomes. Lack of an easy way to share results slows down progress and takes the fun out of being a scientist.

Agree or disagree? What are your top challenges? Let me know in the comments.

I wrote more about the topic here: https://hubs.ly/Q011YdwG0

#ComputationalBiology #ComputationalResearch

I have to admit that I lost track of how many conversations I had last year with computational researchers of all levels and in organizations ranging from tiny to large about the challenges they face every day when doing their jobs. I am grateful for each and every one of these discussions. To say I...

#Epigenomics will be a game changer in precision oncology, according to our friend Dr. Benjamin Haibe-Kains of the Princ...
01/07/2022
Metabolomics or Epigenomics?

#Epigenomics will be a game changer in precision oncology, according to our friend Dr. Benjamin Haibe-Kains of the Princess Margaret Cancer Centre and the viewers we polled. But is there potential for #Metabolomics? What do you think?
https://hubs.ly/Q011J4FC0

Epigenomics will be a game changer in precision oncology, according to our friend Benjamin Haibe-Kains of the Princess Margaret Cancer Center. But is there p...

What’s the optimal Computational Biology team structure? For our friend Yair Benita at CytoReason it looks like this:Com...
01/06/2022
What's the ideal Computational Biology team structure?

What’s the optimal Computational Biology team structure? For our friend Yair Benita at CytoReason it looks like this:
Computational Biologist: - full time
Biologist - full time
Clinician - full or part time
Software Engineer - full or part-time

While it's true these team members don't speak the same language - “model” means one thing to a biologist and another thing to a software engineer - when they work together on one project, they start communicating more closely and come up with ways to tackle the problem and understand each other’s worlds. #ComputationalBiology #BioInformatics
https://hubs.ly/Q011zPw50

What is the ideal structure for Computational Biology teams?For Yair Benita, Head of Science Operations at CytoReason, it looks like this:Computational Biolo...

While machine learning produces more accurate results, it also presents challenges for computation researchers:1. Data s...
01/04/2022
Challenges with Machine Learning in Single Cell Analysis

While machine learning produces more accurate results, it also presents challenges for computation researchers:
1. Data sets are growing exponentially
2. Machine learning frameworks don’t add computational speed
3. Researchers don’t have compatible machine resources required to process large datasets
The solution?
1. Implement faster GPU-accelerated workflows
2. Flexible Dev Ops environments for deploying and viewing models easily
3. Operationalize the computational researcher’s team

#computationalResearch #SingeCell #Genomics #Bioinformatics #ComputationalBiology
https://hubs.ly/Q011r1qW0

While machine learning produces more accurate results, it also presents challenges for computation researchers:1. Data sets are growing exponentially2. Machi...

Why GPU’s are so important in single-cell analysis:1. GPU’s accelerate a process by almost 20X vs. CPU’s2. GPU’s cut cos...
01/03/2022
GPU vs CPU in Single Cell Analysis

Why GPU’s are so important in single-cell analysis:
1. GPU’s accelerate a process by almost 20X vs. CPU’s
2. GPU’s cut costs by 2/3
#GPUAcceleration #SingleCellAnalysis #ComputationalBiology #Bioinformatics
https://hubs.ly/Q011pWKS0

Why GPU’s are so important in single-cell analysis:1. GPU’s accelerate a process by almost 20X vs. CPU’s2. GPU’s cut costs by 2/3 Emily So is an Application ...

Lantern Pharma selects Code Ocean to power AI focused Computational Research and large scale collaborations. Leveraging ...
10/27/2021

Lantern Pharma selects Code Ocean to power AI focused Computational Research and large scale collaborations. Leveraging Code Ocean’s Compute Capsule®, the move will further power Lantern’s RADR® platform @LanternPharma @CodeOceanHQ #AI #Biotechnology #DrugDiscovery https://hubs.ly/H0-7-J00

Reducing the Complexity of Single-Cell #Genomic Analysis #AI #NVIDIAAI #RAPIDSai #AWS #ComputeCapsule #Bioinformatics #C...
10/15/2021

Reducing the Complexity of Single-Cell #Genomic Analysis #AI #NVIDIAAI #RAPIDSai #AWS #ComputeCapsule #Bioinformatics #ComputationalBiology https://hubs.ly/H0Zt22_0

Orchestrating and sharing large #multimodal data for transparent and #reproducible research. @bhaibeka  https://hubs.ly/...
10/07/2021
Orchestrating and sharing large multimodal data for transparent and reproducible research - Nature Communications

Orchestrating and sharing large #multimodal data for transparent and #reproducible research. @bhaibeka https://hubs.ly/H0YZRhS0
All analyses performed can be reproduced with a custom compute capsule on @CodeOceanHQ https://hubs.ly/H0YZVJz0

#Bioinformatics #Biotechnology

It is no secret that a significant part of scientific research is difficult to reproduce. Here, the authors present a cloud-computing platform called ORCESTRA that facilitates reproducible processing of multimodal biomedical data using customizable pipelines and well-documented data objects.

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Provide a one-stop shop where computational research can be created, organized and shared. Learn more: https://ebsco.is/2SMuZoV Code Ocean
Researchers waste precious time performing or waiting on infrastructure and environment setup, configuration, data management, and other operational tasks. Results are often hard to find, reproduce, reuse, and share and computational costs are high. What can be done? Download the brief from Code Ocean to find out: https://ebsco.is/3bT5F6C
Computational research and discovery teams are struggling to keep their work organized, and ready to be used by others. Find out how Code Ocean can help: https://ebsco.is/3hR7Qvk
What an INSANE week we had at EISP! 1 Exit 2 huge successful rounds by 2 alumni 3 awards won The proven track record for EISP just keeps on going!! We are pleased to share this incredible article by CTech, which reviewing Yarden, our Managing Director, and EISP as one of the leading #accelerators in the Israeli #ecosystem >> https://bit.ly/3wjQTxI Poalim Hi-Tech, בנק הפועלים Bank Hapoalim, Adi Hoorvitch Lavi, Yarden Abarbanel, Noa Levcovich, Zeekit, Explorium, Suridata.AI, Code Ocean #startups #entrepreneurship #tech #innovation #industry
A big congrats to Simon Adar from our #204batch, the CEO of Code Ocean, for completing an A round of $21M!!! 👏👏👏 The company goals to assist researchers to replicate data-heavy science and to establish a more collaborative environment at the cutting edge. The A round was led by Battery Ventures, with Digitalis Ventures, EBSCO, and Vaal Partners participating as well as numerous others. Way to go!!💪
Good idea! We will be here a lot!
EBSCO and Code Ocean are pleased to collaborate with the UK Reproducibility Network to help bring reproducibility in computational research. Learn more about using Code Ocean to assist with research: https://ebsco.is/3fRfEdv
EBSCO is supporting open research and reproducibility by teaming up with the UK Reproducibility Network and Code Ocean to help improve the quality of computational research. Try Code Ocean for free: https://ebsco.is/36lbwzi
Does your library provide a service for its researchers to openly collaborate with peers? Learn how protocols.io and Code Ocean can help. https://ebsco.is/34ayR5D
Learn about the benefits of sharing code and data in this interview with Simon Adar from Code Ocean https://ebsco.is/3hlut7k
Help your researchers create, share, publish, preserve and reuse executable code and data. Sign up for an interactive session with Code Ocean: https://ebsco.is/RW62320f
Contact us to plan an interactive session for your researchers on research creation and sharing with Code Ocean: https://ebsco.is/RW61520f