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January 11, 2020

How we integrate science and engineering

The CCDL team includes science, engineering, and design expertise. Combining these three disciplines in different ways across projects enables us to carry out our mission.

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January 11, 2020

Pinning transitive R dependencies for fun and reproducible builds

Like many teams that work with large amounts of external software, we run into issues with our transitive dependencies. In general, transitive dependencies are a hard problem to solve.

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January 11, 2020

Overcoming the steep data science learning curve in childhood cancer research using workshops

Though technology can introduce great benefit into our lives, it is often accompanied by a substantial amount of time and some expected frustration before we can reap the rewards. The time spent learning a new technology is what we usually call a learning curve.

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January 11, 2020

Gene Expression Repositories Explained

The goal of our refine.bio project is to download, process, and make available gene expression datasets that can be analyzed together, or in parts, depending on a researcher’s need. Childhood cancer researchers need to be able to use data generated through multiple profiling technologies including microarrays and RNA-sequencing.

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January 11, 2020

Better Logging in Python

There are countless log blog posts out there about the benefits of good logging, how to log well, and how much to log. Going through them all can be a real log blog slog. Wouldn't it be cool if you could log like this:logger.info("Something happened!", job=job.id, user=user.id) and get an easily searchable output.

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January 11, 2020

Method for the preparation of a caffeine-containing solution from dehydrated magic beans

Caffeine is a stimulant that can induce alertness in certain individuals when consumed at an appropriate quantity. Caffeine is often obtained by ingesting caffeine-containing solutions. However, no protocol for obtaining caffeine from dehydrated, roasted beans using materials typically available in a Philadelphia office has been described in the published literature.

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January 11, 2020

Why ALSF Views Resource Sharing as Important

Alex’s Lemonade Stand Foundation (ALSF) staunchly believes that stronger scientific sharing practices will accelerate the pace of discovery and finding cures for children with cancer. Robust sharing improves reproducibility, minimizes redundant studies and maximizes our return on research investment.

Resources

January 11, 2020

How we set goals

Our particular process is designed to source opportunities from our team members and external stakeholders, convert those opportunities into a set of potential goals, and then select the goals that we expect will most advance our mission.

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January 11, 2020

Automatic scroll restoration in Single Page Applications (SPA)

The ability to restore scroll position is often critical for website usability. It helps users keep the flow of navigation when going back and forth between different pages. Most modern browsers take care of restoring the scroll position automatically, but it doesn’t always work for Single Page Applications where the content is generated on the client’s side, often asynchronously.

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January 11, 2020

How we train: Going remote

When the CCDL (along with everyone else) realized that we would have to conduct our bioinformatics training workshops remotely, we had to make some quick decisions about how we were going to do it. Most of the instructional materials for our in person workshops were already online, so we knew we had a good base to work from. We just needed to figure how to adapt the live instruction.

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January 11, 2020

Why We Must Share Research and Resources

When my daughter Alex was diagnosed with cancer and throughout her battle, we saw how our community of people rallied around our family. No one knew quite how to help, but they were willing to do whatever was needed to ease the burden we faced.

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January 11, 2020

The Childhood Cancer Data Lab's not-so-secret sauce for efficient workflows — aka Philadelphia’s third most famous process

'Work smarter not harder’ is useless advice if you don’t know how to ‘work smarter’. But the Childhood Cancer Data Lab's work and processes may be the smartest I’ve ever had the pleasure of learning and adopting.

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January 11, 2020

Automating analyses with workflow managers

At the Data Lab, we are big proponents of automating the boring stuff so we can spend more time thinking about the fun stuff. But how exactly do we do that, and what does it mean to automate the boring stuff?

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January 11, 2020

Building, Improving, and Collaborating: A Look Back at Training Workshops in 2021

November marked the final Childhood Cancer Data Lab training workshop for 2021. We held four week-long virtual workshops this year, teaching 88 researchers the data science skills they need to examine their own data.

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January 11, 2020

Setting your research up for success in a data driven world

Before working as a Data Scientist at the Childhood Cancer Data Lab, I spent time in my PhD and post-doctoral fellowship in two very different research environments. Each had their own unique way of doing research. I found that some things worked really well and others were not as successful.