Blog


Tools

May 13, 2024

Tools
2024-05-13
Choosing wisely: A behind-the-scenes look at how we selected cell type annotation platforms for the ScPCA Portal

ALLY HAWKINS

So you recently did some single-cell RNA sequencing and are working on analyzing your data. You’ve already quantified the gene expression data, performed any filtering, and normalized your data, but now what? You know you want to perform differential expression analysis or that you need to annotate the cell types found in your data, but there are so many different tools and methods for performing these analyses. How do you know which one is the best method for your dataset? Don’t worry, we’ve all been there – even experts in the single-cell field have been there. 

Resources

May 8, 2024

Resources
2024-05-08
Prototyping process with journey maps

DEEPA PRASAD

The Open Single-cell Pediatric Cancer Atlas (OpenScPCA) is an open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal, which currently holds over 500 samples from over 50 pediatric cancer types. OpenScPCA uses an open contribution model designed to allow experts worldwide to contribute and rapidly share the results of analyses in real time. The project was officially launched in April 2024.

Projects

May 1, 2024

Projects
2024-05-01
Introducing the first community-contributed datasets on the ScPCA Portal!

JEN O'MALLEY

In March 2022, we launched the Single-cell Pediatric Cancer Atlas (ScPCA) Portal to make uniformly processed single-cell and single-nuclei RNA-Seq data widely available to the childhood cancer research community. Initially, all data available on the Portal was generated through grants funded by Alex’s Lemonade Stand Foundation (ALSF) as part of the ScPCA project. But enabling access to ALSF-funded data was just the beginning of our vision.Sharing is key to ensuring the Portal’s continued growth. Our sights were set on allowing more pediatric cancer researchers to contribute data to the ScPCA Portal.

Projects

April 23, 2024

Projects
2024-04-23
Introducing the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) Project!

JEN O'MALLEY

The Data Lab has just launched the brand new Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project! This open, collaborative project aims to analyze data from the ScPCA Portal, which currently holds 500 samples from over 50 pediatric cancer types. We are seeking contributors with diverse skills and expertise to join the project!

Announcements

April 12, 2024

Announcements
2024-04-12
Full: Data Lab Single-Cell RNA-Seq Workshop, Virtual, June 10-14, 2024

JEN O'MALLEY

We are excited to announce that our next virtual workshop, Introduction to Single-cell RNA-Seq, will run from June 10-14, 2024! In this workshop, Data Lab staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, single-cell RNA-seq data analysis, and annotating cell types.

Announcements

April 5, 2024

Announcements
2024-04-05
Full: Data Lab Reproducible Research Practices and Introduction to OpenScPCA Workshop, Philadelphia, May 14-15, 2024

JEN O'MALLEY

Applications are open for the Data Lab's next workshop! We are holding a two-day course on Reproducible Research Practices and the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project from May 14-15, 2024. Please note that the OpenScPCA module is an optional part of the workshop. The course begins with an introduction to principles and techniques to achieve reproducible results in computational cancer research. On day two, you can choose to continue the workshop and learn how to put your skills to use for OpenScPCA, our new pediatric cancer research project.

Announcements

March 6, 2024

Announcements
2024-03-06
Alex’s Lemonade Stand Foundation at AACR 2024: Resources, tools, and opportunities for pediatric cancer researchers

JEN O'MALLEY

Are you attending the American Association for Cancer Research (AACR) annual meeting in San Diego, CA? Visit the Alex’s Lemonade Stand Foundation (ALSF) Grants and Data Lab teams at booth 3755 in the exhibit hall from April 7-10 and during poster sessions on April 8. We will announce a new collaborative project and share exciting news about the Single-cell Pediatric Cancer Atlas Portal and training opportunities!

News

February 11, 2024

News
2024-02-11
Meet the women who integrate science, engineering, and design at the Childhood Cancer Data Lab

JEN O'MALLEY

Did you know that 70% of the Alex’s Lemonade Stand Foundation (ALSF) Childhood Cancer Data Lab team are currently women? Advancing our mission to empower childhood cancer researchers with knowledge, data, and tools would not be possible without their expertise. On the International Day of Women and Girls in Science, we are excited to introduce you to these women who integrate science, engineering, and design to tackle some of the greatest challenges faced by the pediatric cancer research community!

Tools

December 18, 2023

Tools
2023-12-18
Don't Make Me Write: Tips for Avoiding Typing in RStudio

STEPHANIE SPIELMAN

I have a confession to make: I am lazy. Ok, maybe that's too strong. Let's go for a euphemism instead: I am efficient. I love learning handy tricks that make my life easier and make my job smoother with fewer hiccups along the way. This is one part of why, here in the Data Lab, we love automation - why waste our time on rote, repetitive, housekeeping tasks when we can get the bots to do it for us? In this blog post, we'll highlight a few tips about how you can use RStudio to code more efficiently.

Resources

November 15, 2023

Resources
2023-11-15
Git workflows for scientific projects and when we use them

JACLYN TARONI

Writing source code is a significant part of data-intensive biomedical research. Everything from cleaning and pre-processing data to generating publication figures can be accomplished programmatically. Increasingly, funding agencies and journals require researchers to share their code. To pick a few examples, the Data Lab’s parent organization, Alex’s Lemonade Stand Foundation (ALSF), has such a requirement for awardees, and PLoS Computational Biology requires authors to make code underlying results and conclusions available.

Resources

September 18, 2023

Resources
2023-09-18
I’m terrible with names…but I’m using ontologies to try to be better

JOSHUA SHAPIRO

There is an old joke in computer science about how there are only two hard things: cache invalidation, naming things, and off-by-one errors. I’ll leave aside the first one as beyond my own expertise, but the second comes up all the time in my work as a biological data scientist. Naming variables and functions in my code is a constant struggle, but one I have to deal with on my own or with my team. Much bigger problems come up when trying to deal with all the various ways that people across the world use names when talking about the diseases they work on, the types of cells they are looking at, the experimental methods they are using, and just about every other aspect of their studies.

Announcements

August 16, 2023

Announcements
2023-08-16
Full: Data Lab Reproducible Research Practices Workshop, Philadelphia, October 24-25, 2023

JEN O'MALLEY

Applications are open for the Data Lab's next workshop! We will be holding a Reproducible Research Practices Course in-person on October 24-25, 2023. Instructors will introduce principles and techniques to achieve reproducible results in computational cancer research. We’ll show you the fundamentals of commonly-used approaches in reproducibility that you can apply to increase the impact of your research by making your findings more robust and reliable! To ensure that workshop attendees have a great hands-on experience, there will be a very limited number of seats available.

Projects

July 31, 2023

Projects
2023-07-31
Collaborating with the Data Lab on OpenPBTA shaped how our team works reproducibly

JO LYNNE ROKITA

At the Center for Data-Driven Discovery in Biomedicine (D3b), I lead the Bioinformatics Translational Pediatric Oncology Team, a team of bioinformatics scientists. Our mission is to advance pediatric oncology research and precision medicine through collaboration and development of open-source analytical tools, frameworks, and data resources. In 1998, I lost my four year old cousin John Matthew to a brain tumor we now know was likely a diffuse intrinsic pontine glioma. So, it was bittersweet for me to see the Open Pediatric Brain Tumor Atlas (OpenPBTA) manuscript published in Cell Genomics on the last day of brain tumor awareness month this past year. But let’s rewind.

Resources

May 18, 2023

Resources
2023-05-18
Don't Make Me Read: Tips for Writing Effective Documentation

DEEPA PRASAD

Writing effective documentation is challenging. Users might not always read every word in the documentation. They might even just scroll past large chunks of text, but we can accommodate those behaviors by structuring and formatting content appropriately.

Announcements

May 15, 2023

Announcements
2023-05-15
The Single-cell Pediatric Cancer Atlas (ScPCA) Portal is now accepting dataset submissions!

JEN O'MALLEY

In 2019, Alex’s Lemonade Stand Foundation (ALSF) established the Single-cell Pediatric Cancer Atlas (ScPCA) through awards for data generation and to create an atlas of single-cell gene expression profiles of pediatric cancers of different types and from different organ sites. The Data Lab launched the ScPCA Portal in 2022 to make uniformly processed, summarized single-cell and single-nuclei RNA-seq data and de-identified metadata available for download. The ScPCA Portal also supports other data modalities, such as bulk RNA-seq, CITE-seq, and spatial transcriptomics. The ScPCA Portal currently hosts data for over 500 pediatric tumor and patient-derived xenograft samples from more than 50 cancer types, and continues to grow. The Data Lab is seeking contributions to the ScPCA Portal from researchers with existing single-cell datasets.

Announcements

May 4, 2023

Announcements
2023-05-04
Full: Data Lab Single-Cell RNA-Seq Workshop, Philadelphia area, June 13-15, 2023

JEN O'MALLEY

We are excited to announce that our next workshop, Introduction to Single-cell RNA-Seq, will take place in-person from June 13-15, 2023! Data Lab staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, single-cell RNA-seq data analysis, annotating cell types, and more. The 3-day course will take place from 9am-5pm Eastern time in Bala Cynwyd, PA, just outside of Philadelphia. Travel reimbursement (up to a certain amount) is available for qualifying participants.

Projects

April 11, 2023

Projects
2023-04-11
Downstream Analysis Workflows – do you have a list of genes whose expression you are particularly interested in?

CHANTE BETHELL

The Childhood Cancer Data Lab maintains a collection of uniformly processed single-cell data from pediatric cancer clinical samples and xenografts in the Single-cell Pediatric Cancer Atlas (ScPCA) Portal. Although access to preprocessed data saves researchers time, we know that the downloads from the ScPCA Portal are only the starting point. That’s why we’ve created downstream analysis workflows for commonly performed analyses. Instead of writing code wholesale, you can analyze data once you’ve configured these workflows.

Announcements

March 28, 2023

Announcements
2023-03-28
Full: Data Lab Single-Cell RNA-Seq Workshop, Virtual, May 15-19, 2023

JEN O'MALLEY

We are excited to announce that our next virtual workshop, Introduction to Single-cell RNA-Seq, will run from May 15-19, 2023! In this workshop, Data Lab staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, single-cell RNA-seq data analysis, and annotating cell types.

Tools

March 14, 2023

Tools
2023-03-14
Creating an open source workflow to uniformly process data for the Single-cell Pediatric Cancer Atlas portal

ALLY HAWKINS

Last year, the Data Lab launched the Single-cell Pediatric Cancer Atlas (ScPCA) Portal, which today holds uniformly processed single-cell gene expression data obtained from 8 separate labs, over 480 samples, and representing 38 cancer types. The portal is still growing as we continue to receive and process raw data from ScPCA investigators! All uniformly processed data is made available for download on the ScPCA Portal, giving researchers easy access to a growing database of summarized gene expression data and metadata to utilize for their own research. But how exactly did we make sure that all of the data was uniformly processed? And how are we able to ensure uniform processing for incoming samples as the portal continues to grow?

Announcements

February 27, 2023

Announcements
2023-02-27
Visit Alex's Lemonade Stand Foundation at AACR 2023!

JEN O'MALLEY

Are you attending the American Association for Cancer Research (AACR) annual meeting in Orlando, FL this year? Visit Alex's Lemonade Stand Foundation (ALSF) at booth 369 in the exhibit hall from April 16-19! You'll find information about ALSF's grants program, the Childhood Cancer Data Lab and more. The Data Lab will also be holding office hours during select time slots.

Announcements

February 10, 2023

Announcements
2023-02-10
Full: Data Lab Advanced Single-Cell RNA-Seq Workshop, Virtual, March 13-17, 2023

JACLYN TARONI

The Data Lab is excited to announce that our next training workshop will be held virtually from March 13-17, 2023! During this workshop, we will cover advanced topics in the analysis of single-cell RNA-seq data for researchers studying pediatric cancer. The workshop will take place each day from 12-5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with our staff available for consultation. You’ll need a laptop with internet access and to install Zoom and Slack. You will log into an RStudio Server hosted by the Data Lab from your web browser. Pediatric cancer researchers are encouraged to apply now!

Projects

January 20, 2023

Projects
2023-01-20
Lessons learned from working reproducibly with others

JACLYN TARONI

In September 2022, the Open Pediatric Brain Tumor Atlas (OpenPBTA) project culminated (for now) in a preprint on bioRxiv. This project, started in late 2019 and co-organized with the Center for Data Driven Discovery in Biomedicine (D3b) at Children’s Hospital of Philadelphia (CHOP), is a collaborative effort to comprehensively describe the Pediatric Brain Tumor Atlas (PBTA), a collection of multiple data types from tens of tumor types (read more about why crowdsourcing expertise for the study of pediatric brain tumors is important here). The project is designed to allow for contributions from experts across multiple institutions. We’ve conducted analysis and drafting of the manuscript openly on the version-control platform GitHub from the project’s inception to facilitate those contributions.

Tools

January 5, 2023

Tools
2023-01-05
A clustering analysis workflow for use with your ScPCA dataset!

JEN O'MALLEY

Recently, we told you about the Single-cell Pediatric Cancer Atlas (ScPCA) downstream analysis workflow. This ready-to-go workflow is intended to be used with single-cell and single-nuclei gene expression data available on the ScPCA Portal. We developed this workflow to filter, normalize, and perform dimensionality reduction, as well as incorporate initial clustering results to each processed sample/library object. Now we’re excited to introduce one of our latest offerings for use with ScPCA data, a clustering analysis workflow, which can be applied to datasets after running the filtering, normalization, and dimensionality reduction workflow! 

Announcements

December 1, 2022

Announcements
2022-12-01
Full: Data Lab Advanced Single-Cell RNA-Seq Workshop, Philadelphia area, January 31-February 2, 2023

JEN O'MALLEY

The Data Lab is excited to announce that our next training workshop will be held in-person from January 31-February 2, 2023! During this workshop, we will cover advanced topics in the analysis of single-cell RNA-seq data for researchers studying pediatric cancer. The 3-day course will take place from 9am-5pm Eastern time in Bala Cynwyd, PA, just outside of Philadelphia. Travel reimbursement is available for qualifying participants. 

Resources

November 30, 2022

Resources
2022-11-30
Scientific Community Bulletin: What’s happening in December?

JEN O'MALLEY

Welcome to the Data Lab’s December Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!

Projects

November 7, 2022

Projects
2022-11-07
refine.bio refactoring and Web Accessibility

NOZOMI ICHIHARA

In this blog post, I’d like to give an overview of the refine.bio refactoring process and web accessibility considerations. Through this process, our goal is to enhance the site usability and performance by improving the code quality and making the application more accessible. But before going into more details about them, let me provide you a quick history of refine.bio. 

Resources

October 31, 2022

Resources
2022-10-31
Scientific Community Bulletin: What’s happening in November?

JEN O'MALLEY

Welcome to the Data Lab’s November Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!

Resources

October 6, 2022

Resources
2022-10-06
Cataloging the CCDI Childhood Cancer Data Catalog (CCDC)

STEPHANIE SPIELMAN

Here at the Data Lab, we're all about, well, data! We believe that data sharing and accessibility is key to accelerating the research process, and ultimately to improving outcomes for childhood cancer patients. So, we were excited to learn that one of the goals of the NCI/NIH initiative, the Childhood Cancer Data Initiative (CCDI), is to build up a Data Ecosystem that will facilitate pediatric cancer researchers' ability to explore and collect data from disparate resources. Although this Ecosystem is still in the early stages, several components are already being developed and are available for researchers to use! One component that is particularly interesting to us is the CCDI's Childhood Cancer Data Catalog (CCDC).

Resources

October 3, 2022

Resources
2022-10-03
Scientific Community Bulletin: What’s happening in October?

JEN O'MALLEY

Welcome to the October Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!

Resources

September 2, 2022

Resources
2022-09-02
Scientific Community Bulletin: What's happening in September?

JEN O'MALLEY

Welcome to the September Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!

Projects

August 29, 2022

Projects
2022-08-29
Introducing the ScPCA downstream analysis workflow!

CHANTE BETHELL

At the Data Lab, we are constantly looking for ways to enhance the tools we build for pediatric cancer researchers. Earlier this year, we launched the Single-cell Pediatric Cancer Atlas portal, a database of uniformly-processed single-cell data from pediatric cancer clinical samples. One way we felt the portal could be even more beneficial to pediatric cancer researchers is with a ready-to-go workflow that takes in single-cell data and prepares it for downstream analyses such as unsupervised clustering. 

Announcements

August 16, 2022

Announcements
2022-08-16
Full: Data Lab Single-Cell RNA-Seq Workshop, Virtual, September 19-23, 2022

JEN O'MALLEY

The Data Lab is excited to announce our next virtual workshop running from September 19-23, 2022! In this workshop, Data Lab staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, single-cell RNA-seq data analysis, and pathway analysis.

Projects

August 10, 2022

Projects
2022-08-10
Teaching with live coding in R and RStudio

JOSHUA SHAPIRO

The Data Lab teaches data science courses targeted toward pediatric cancer researchers that introduce topics such as analysis of gene expression in bulk and single-cell data and principles of reproducible research. I wrote previously about how we use RStudio Server for our remote courses to simplify setup, and I wanted to write a bit more about some of the instructional practices we use so that our participants get the best experience we can provide. In particular, I wanted to talk about our use of live coding to facilitate active learning, and one of the tools we developed to make our course development just a bit easier.

Resources

August 1, 2022

Resources
2022-08-01
Scientific Community Bulletin: What's happening in August?

JEN O'MALLEY

Welcome to the August Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations.

Resources

July 27, 2022

Resources
2022-07-27
Queueing Javascript Promises

DAVID MEJIA

Often when building a server-client web application, we will encounter a situation where we want to send requests to our API in the chronological order that they occur on the client. Due to the asynchronous nature of these requests, it might not be possible to send them in the same callback for the event that triggered them. This is because we want to use the response from the previous request to craft our current one. A solution to this problem would be to implement a queue. Instead of calling the API immediately after events occur, implementing a queue ensures the latest data is sent with any request.

Resources

July 6, 2022

Resources
2022-07-06
Scientific Community Bulletin: What's happening in July?

JEN O'MALLEY

Welcome to the July Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!

Tools

June 13, 2022

Tools
2022-06-13
How we use renv to be in two places at once

JACLYN TARONI

At the Data Lab, our science team has a practice where an individual team member shares something that they recently figured out (or didn’t totally figure out yet) on a biweekly basis. We call this short 5-10 minute presentation How I Solved This, and it’s a great way to formally share (often hard-won) knowledge with each other. In this post, we thought we’d share how we solved something with the `renv` package with you.

Resources

June 2, 2022

Resources
2022-06-02
Scientific Community Bulletin: What’s happening in June?

JEN O'MALLEY

Welcome to the Childhood Cancer Data Lab’s new blog feature, the monthly Scientific Community Bulletin! At the start of each month, we will share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Our goal is to promote learning opportunities and highlight some of the excellent resources that our community provides.

Tools

May 4, 2022

Tools
2022-05-04
Strategies to center user needs for research tools

DEEPA PRASAD

The Childhood Cancer Data Lab builds resources guided by the most pressing needs of our primary users: pediatric cancer researchers. As the Data Lab's UX Designer, I conduct research activities with scientists like usability evaluations, semi-structured interviews, and card sorts to gain insight into their activities, processes, pain-points, and behaviors. I work with scientists and engineers at the Data Lab to use this information to improve existing products and services or to create new ones.

Announcements

May 2, 2022

Announcements
2022-05-02
Data Lab Reproducibility Workshop, Philadelphia area, June 10, 2022

JEN O'MALLEY

The Data Lab is excited to announce that our next training workshop is taking place in-person on Friday, June 10, 2022! During this full day workshop, instructors will introduce principles and techniques to achieve reproducible results in computational cancer research. We’ll show you the fundamentals of commonly-used approaches in reproducibility that you can apply to increase the impact of your research by making your findings more robust and reliable!

Announcements

April 12, 2022

Announcements
2022-04-12
Welcome to the Data Lab’s newly renovated website

JEN O'MALLEY

The Childhood Cancer Data Lab is growing as a resource for pediatric cancer researchers and we have more to offer to our community now, than ever before. Transitioning to our new and improved website is an exciting milestone, and here, we look forward to sharing progress, introducing new initiatives, and cultivating more opportunities to support childhood cancer research. Welcome to our new virtual home!

Projects

March 28, 2022

Projects
2022-03-28
Introducing the Single-cell Pediatric Cancer Atlas (ScPCA) Portal

JEN O'MALLEY

The Single-cell Pediatric Cancer Atlas (ScPCA) project began in 2019 when Alex’s Lemonade Stand Foundation (ALSF) funded 10 awards for single-cell profiling of pediatric cancer samples. The goal was to produce an atlas of gene expression profiles for a variety of childhood cancer types from different organ sites.

Resources

February 24, 2022

Resources
2022-02-24
Automating analyses with workflow managers

ALLY HAWKINS

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?

Announcements

February 11, 2022

Announcements
2022-02-11
Full: Data Lab Single-Cell RNA-Seq Workshop, Virtual, March 14-18, 2022

JEN O'MALLEY

The Data Lab will hold our first virtual workshop of the year from March 14-18, 2022!In this workshop, we will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, single-cell RNA-seq data analysis, and pathway analyses.

Resources

December 14, 2021

Resources
2021-12-14
Setting your research up for success in a data driven world

ALLY HAWKINS

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.

Resources

November 17, 2021

Resources
2021-11-17
Building, Improving, and Collaborating: A Look Back at Training Workshops in 2021

JEN O'MALLEY

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.

Resources

October 20, 2021

Resources
2021-10-20
The Childhood Cancer Data Lab's not-so-secret sauce for efficient workflows — aka Philadelphia’s third most famous process

CANDACE SAVONEN

'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.

Resources

October 5, 2021

Resources
2021-10-05
Why We Must Share Research and Resources

LIZ SCOTT

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.

Announcements

September 28, 2021

Announcements
2021-09-28
Full: CCDL Single-Cell RNA-Seq Workshop, Virtual, November 1st-5th, 2021

JEN O'MALLEY

The workshop will take place on November 1-5, 2021 from noon to 5pm eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with our staff available for consultation.

Projects

August 25, 2021

Projects
2021-08-25
Introducing Example Analyses for Use with refine.bio Data

JEN O'MALLEY

Introducing refine.bio examples. Here, users can access a variety of example analyses implemented in R, such as clustering and heat maps, differential expression analysis, and pathway analysis, for use with refine.bio data.

Announcements

July 28, 2021

Announcements
2021-07-28
Full: CCDL RNA-Seq Workshop, Virtual, September 20th - 24th, 2021

JEN O'MALLEY

The workshop will take place on September 20 - 24, 2021 from noon - 5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation.

Announcements

May 25, 2021

Announcements
2021-05-25
The Hack4Rare Event in June/July 2021

CHANTE BETHELL

Hack4Rare is a virtual event that calls for healthcare startups, developers, solutions architects, and hackathon enthusiasts to join researchers, clinicians and patients in developing solutions built around a number of rare diseases including neurofibromatosis, PTEN Hamartoma Tumor Syndrome, RASopathies and Desmoid Tumors.

Announcements

May 21, 2021

Announcements
2021-05-21
Full: CCDL Single-Cell RNA-Seq Workshop, Virtual, June 28th - July 2nd, 2021

CHANTE BETHELL

The workshop will take place on June 28- July 2, 2021 from noon to 5pm eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation.

Announcements

February 15, 2021

Announcements
2021-02-15
Full: CCDL RNA-Seq Workshop, Virtual, March 22nd - 26th, 2021

CHANTE BETHELL

The workshop will take place on March 22 - 26, 2021 from noon - 5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation

Announcements

September 22, 2020

Announcements
2020-09-22
The Hack for NF Event in October/November 2020

CASEY GREENE

At Alex’s Lemonade Stand Foundation’s Childhood Cancer Data Lab, we’re excited to be helping out with an upcoming event hosted by the Children’s Tumor Foundation. If you participate, you may meet members of our team who are mentoring and judging.

Resources

August 18, 2020

Resources
2020-08-18
How we train: Going remote

JOSHUA SHAPIRO

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.

Announcements

June 1, 2020

Announcements
2020-06-01
Full: CCDL RNA-Seq Workshop, Virtual, June 22nd - 26th, 2020

GUEST USER

The workshop will take place on June 22 - 26, 2020 from noon - 5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation.

Projects

May 29, 2020

Projects
2020-05-29
OpenPBTA: Someone is wrong on the internet and it’s probably us (updated 9-9-2020)

JACLYN TARONI

Here at the Childhood Cancer Data Lab, we value transparency and the practice of open science. Much of the work we’ve done and the products that we build hinge on the generosity and openness of other scientists. In this post, as part of National Brain Tumor Awareness month, we want to talk about a project that our science team has been working on over the last few months (and to do so in a way that aligns with our values).

Announcements

April 20, 2020

Announcements
2020-04-20
Full: CCDL RNA-Seq Workshop, Virtual Pilot, May 4-8th, 2020

JACLYN TARONI

We know that pandemic-related university closures mean that the demand for opportunities for pediatric cancer researchers to increase their analytical skills has never been higher. As such, we are delighted to announce a pilot virtual workshop running from May 4-8, 2020!

Projects

April 8, 2020

Projects
2020-04-08
3 things the CCDL is doing right now to keep pediatric cancer research moving forward

JACLYN TARONI

To help keep pediatric cancer research moving forward, here are 3 ways the CCDL is helping the research community during this time: refine.bio, virtual workshops, and the Open Pediatric Brain Tumor Atlas project.

Announcements

February 25, 2020

Announcements
2020-02-25
POSTPONED: Visit the Childhood Cancer Data Lab at Booth 1601 at AACR 2020!

JACLYN TARONI

The CCDL will have a team of scientists at the American Association for Cancer Research 2020 Annual Meeting in sunny San Diego! Our team members are excited to talk to researchers studying pediatric cancer at Booth 1601.

Announcements

February 10, 2020

Announcements
2020-02-10
Carnegie Mellon University Libraries RNA-Seq Workshop, Pittsburgh PA

JOSHUA SHAPIRO

Carnegie Mellon University Libraries is partnering with the Childhood Cancer Data Lab (CCDL), founded by Alex’s Lemonade Stand Foundation, to host a Data Analysis workshop using CCDL materials.

Resources

January 30, 2020

Resources
2020-01-30
How we set goals

KURT WHEELER

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.

Projects

January 9, 2020

Projects
2020-01-09
Exploring neurofibromatosis data with refine.bio

CASEY GREENE

I’m a scientist at Sage Bionetworks, a nonprofit research organization in Seattle, WA. My work focuses on a family of rare pediatric diseases (NF): neurofibromatosis type 1, type 2, and schwannomatosis.

News

December 19, 2019

News
2019-12-19
2019 In Review: Highlights from the CCDL

CASEY GREENE

This year was a big one for the CCDL. In our mission to empower pediatric cancer experts poised for big discoveries with the knowledge, data and methods to reach them we launched a software product, developed and delivered training workshops on single-cell and bulk RNA-seq analysis, and hired our data science team among other milestones.

Projects

November 19, 2019

Projects
2019-11-19
Does Bulk Tissue Still Belong in a Single-Cell Atlas?

CASEY GREENE

Earlier this year, Alex’s Lemonade Stand Foundation identified single-cell gene expression profiling as an opportunity to build an atlas of cell types within tumors that could be broadly reused by pediatric cancer researchers.

Resources

October 30, 2019

Resources
2019-10-30
Why ALSF Views Resource Sharing as Important

ANNA GREENE

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

October 23, 2019

Resources
2019-10-23
Method for the preparation of a caffeine-containing solution from dehydrated magic beans

JACLYN TARONI

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.

Resources

September 30, 2019

Resources
2019-09-30
How we integrate science and engineering

DEEPA PRASAD, CASEY GREENE

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.

News

August 19, 2019

News
2019-08-19
Reflections on the Childhood Cancer Data Initiative Symposium

JACLYN TARONI, ANNA GREENE

Here at the CCDL we value putting publicly available data to work. For example, we are currently processing and normalizing 1.5 million publicly available gene expression samples totaling ~$1.5 billion research dollars expended.

Resources

August 9, 2019

Resources
2019-08-09
Pinning transitive R dependencies for fun and reproducible builds

WILL VAUCLAIN

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.

Resources

July 25, 2019

Resources
2019-07-25
Overcoming the steep data science learning curve in childhood cancer research using workshops

CANDACE SAVONEN

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.

Announcements

July 10, 2019

Announcements
2019-07-10
CCDL RNA-Seq Workshop, Philadelphia, PA. Oct 14-16th, 2019

CANDACE SAVONEN

The workshop will last from 9AM to 5PM on October 14th, 15th, and 16th at the CCDL offices at 1429 Walnut St Philadelphia, PA, 19102.

Projects

July 1, 2019

Projects
2019-07-01
How does big data help us tackle childhood cancer?

JACLYN TARONI

MultiPLIER is a machine learning approach that brings big data to bear on rare diseases. It’s also an example of the scientific approach and ethos of the CCDL, and the publication is a great opportunity to share how the CCDL is developing new technologies to accelerate research into cures for childhood cancers!

Announcements

June 17, 2019

Announcements
2019-06-17
CCDL RNA-Seq Workshop, Bay Area, CA. Sept 3-5, 2019

CANDACE SAVONEN

The Childhood Cancer Data Lab powered by Alex's Lemonade Stand Foundation is hosting a workshop to introduce childhood cancer researchers to reproducible analysis of bulk and single-cell transcriptomic data.

News

May 28, 2019

News
2019-05-28
17 Reasons to Work at the CCDL

DEEPA PRASAD, ARIEL RODRIGUEZ ROMERO, CANDACE SAVONEN, JACLYN TARONI, KURT WHEELER

The Childhood Cancer Data Lab (CCDL), an initiative of Alex's Lemonade Stand Foundation develops tools, trainings, and methods to empower childhood cancer researchers. The work at the CCDL is focused and impactful. There are multiple opportunities and challenges for you to apply and grow your skills as a scientist or as an engineer.

Announcements

April 25, 2019

Announcements
2019-04-25
CCDL RNA-Seq Workshop, Chicago, IL. June 24-26, 2019

CASEY GREENE

The Childhood Cancer Data Lab powered by Alex's Lemonade Stand Foundation is hosting a workshop to introduce childhood cancer researchers to reproducible analysis of bulk and single-cell transcriptomic data.

News

April 25, 2019

News
2019-04-25
The Workshop that Turns Researchers into Data Wizards

ADAM PARIS

At this hands-on, 3-day session held in Houston, researchers learned data science skills that could accelerate their own work. Drawing on skills learned at the workshop, childhood cancer researchers can perform basic analyses of their work to make informed decisions on how to proceed with their own research. Don’t just take our word for it, though. Read more about the workshop’s incredibly valuable benefits through its attendees’ perspectives.

Projects

April 12, 2019

Projects
2019-04-12
A Desperate Plea for a Free Software Alternative to Aspera

RICH JONES

I work at the Childhood Cancer Data Lab, where we use very big data to find cures for childhood cancers. To move data around the internet at very high speeds, we are forced to use a proprietary software suite called Aspera. If somebody could make a Free Software alternative, the future of the internet would be way more awesome! Best of all, you can be the one to do it!

Resources

March 28, 2019

Resources
2019-03-28
Gene Expression Repositories Explained

KURT WHEELER

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.

Resources

February 28, 2019

Resources
2019-02-28
Better Logging in Python

KURT WHEELER

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.

Resources

January 31, 2019

Resources
2019-01-31
Automatic scroll restoration in Single Page Applications (SPA)

ARIEL RODRIGUEZ

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.

Announcements

January 25, 2019

Announcements
2019-01-25
CCDL RNA-Seq Workshop, Houston TX. March 27-29, 2019

CASEY GREENE

Projects

January 9, 2018

Projects
2018-01-09
refine.bio, Part 2

KURT WHEELER

Projects

September 6, 2017

Projects
2017-09-06
refine.bio, Part 1

KURT WHEELER

Announcements

July 27, 2017

Announcements
2017-07-27
Hello World!

CASEY GREENE

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