A Desperate Plea for a Free Software Alternative to Aspera
Too Long, Didn’t Read
tl;dr: 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!
A Big Data Transfer Protocol
For the past thirty years, the web’s HTTP protocol has been really great at serving things like web pages, chat messages, images, and other objects at the kilobyte to megabyte scale. Unfortunately, the web was not designed for the “big data” objects of today - genetic sequences, large databases, high definition media, and other files at the terabyte to petabyte scale. HTTP transfers over the open internet are hampered by constant connection re-establishment and TCP overhead. Some reconnection problems have been addressed in HTTP/2, but not the overall throughput issues.
The fact is, for very large files, HTTP is slow.
However, there is an alternative, proprietary protocol - FASP, the Fast and Secure Protocol - more known commonly by the client/server software product name Aspera, which avoids these problems. Aspera can deliver speeds up to 1000x times faster than HTTP/FTP. I honestly didn’t believe it until I saw it for myself. In fact, I had never even heard of Aspera before I started this job, and there wasn’t even an English-language Wikipedia article for FASP yet - although I’ve since written one.
Out of necessity, many organizations are now using this proprietary software for large data transfers, including public institutions such as the National Institute of Health, the European Genome Archive/Sequence Read Archive, the National Cancer Institute/cancer.gov, FEMA and private companies, such as Amazon, Netflix and the owner of Aspera, IBM. Basically, if you’re working at terabyte scale, you probably need this software.
Demonstration
Let me reproduce an experiment for you. We’re going to download an experiment’s worth of RNA-Seq expression data from the Sequence Read Archive, which offers both FTP and Aspera downloads. On the left is FTP with wget, which starts first, and on the right the Aspera client, ascp. This test was performed on two different EC2 instances in us-east-1, fetching a 343MB FASTQ file from the Sequence Read Archive, which is in the UK.
As you can see, the ASCP client performs over 200x faster than FTP, and can download the whole file in 9 seconds. It’s pretty magical.
It’s also necessary for our project’s basic feasibility. Without Aspera, it would take us months to years to download the millions of samples like this that we need to process. We’d have to fly all over the world with suitcases full of hard drives to be able to collect our data!
A Proprietary Protocol, a Free Software Solution
In theory, the protocol is simple-ish. The client establishes an SSH connection to the server for negotiating the control of data flow, and then a range of UDP ports above 33001, one for each connection thread, are used to transmit a unidirectional transfer of data, and requests for retransmission are sent back over the SSH connection.
I say in theory, however, because the software is proprietary. So, I have no way of knowing what the protocol is actually doing during a file transfer, just as I have no way of knowing what the client software is doing to my laptop, or what the server software is doing to my servers.
Aspera is owned by IBM - does their client spy on what else is running on my system and report it back to their headquarters as business intelligence? If asked, would they share this information with the government? Without the source code, it’s impossible to tell!
Those were things people used to worry about in the very early days of the internet, until the invention of the Apache web server, which, along with GNU/Linux, truly democratized the web and allowed the explosion of growth which we all benefitted from.
I think a Free Software implementation of Aspera, or something similar, will cause a similar revolution for big data.
Implications
There are obviously many immediate practical implications for having a Free FASP client/server/library implementation.
Science
Firstly, and most relevantly to our work at the Childhood Cancer Data Lab, biologists, physicists and other scientists who deal with “big data” won’t have to use proprietary software to retrieve and share the data they need in a timely fashion. That alone would be a massive boost for science, for software freedom and for data sharing everywhere. But the benefits don’t stop there!
Technology
There are also massive implications for system administrators and software developers. For example, many organizations have moved to using Docker images as part of their system deployments, and although the best practice is to have these images be as small as possible, in practice, this is rarely the case. Images can balloon up to be many tens or even hundreds of gigabytes, especially if they contain large machine learning models or training datasets.
How many thousands of hours of engineer time have already been wasted waiting for slow pulls from DockerHub? A switch to FASP could cut hours down into seconds.
Business
There are also large business implementations. Global businesses who need to share large amounts of data across different regions, especially if that data has to be transferred over the open internet, could massively benefit from radically faster transfers - and in fact, this is IBM/Aspera’s business model!
Filesharing
Although the nature of the protocol makes it difficult to use on some personal networks, I do think that elements of the technology could benefit consumer file-sharing, which has not had any major revolutions since the adoption of BitTorrent in the early 2000s - nearly 20 years ago! BitTorrent isn’t actually too dissimilar to Aspera, so maybe a free FASP implementation would end up replacing or amending file locker services like Mega, which serve massive files over HTTP - do you want to be the next Kim Dotcom? A detailed showdown of BitTorrent versus Aspera would also be really useful for understanding this problem space.
Publishing
Lastly, and definitely not least, I think this project could significantly benefit journalism and publishing.
We are entering the age of big data journalism, and I think the start of that era has been marked by the publishing of the Panama Papers, which was 2.7 terabytes of leaked information. Leaking that over HTTP/FTP upload could take weeks!
In the future, more and more investigative journalism will be driven by leaks of databases and the publishing of massive caches of documents. Currently, the best way that I know of to transfer 2.7TB is to send a bunch of external hard drives in the post. With better FASP Free infrastructure, that won’t be the case forever.
Approaching the Problem
I see two approaches to solving this problem - a reverse-engineering solution and a “clean room” solution. The FASP protocol is not publicly documented, and the technology itself is patented (with a misspelling in the patent title), which may scare off some of the usual suspects like Redhat or Google from developing this technology further.
So, it’s up to us hackers!
Reverse Engineering
The first approach would be to reverse engineer the protocol to create a Free client that can speak to existing servers. This would be immediately useful to us at the CCDL, as we’re not able to distribute proprietary software in our Docker images, so we have to re-run the Aspera installer for every server we instantiate, which costs us time and money.
From there, a server compatible with the Free client could be created and made to work in tandem with the Free client. This would then benefit us at the CCDL as well, as we want to share our massive dataset with other cancer researchers and machine learning researchers without having to use AWS S3’s HTTP methods.
Although this method is probably easier, and perhaps more immediately useful, it may make the lawyers nervous, which could hinder business adoption in the long term, and it also leaves the broader community without a Free protocol specification.
Clean-Room
An alternative approach would be to ignore the existing Aspera server and client implementations and to try to define a new transmission protocol which solves the same problem at the same level of performance without directly copying the methods.
This method will probably have a higher risk of overall project failure as the timeframe will be longer and the amount of cooperation required will be a lot higher, but the ultimate product would be better: a new, Free protocol and reference client/server implementations to power the future of big data file transfers. This way, we’re not limited by the restrictions of Aspera as it stands, and we can potentially add new features, such are parallel endpoints and content discovery.
It could be you!
Now, here’s the really exciting part: You could be the one to do it!
If you’re a great developer who loves free software but has never been a leader of a major Free software project, I strongly encourage you to try it! It won’t lead you to riches (outside of healthy consulting fees), but it can certainly lead you to awesome grant opportunities, chances to travel internationally for free to speak at conferences, lots of new friends, and it will greatly improve your programming, project management and team leadership skills. Give it a shot!
Maybe you’re working on a CS masters degree and are looking for a thesis project? Maybe your company uses Big Data and gives you 20% time to work on whatever you like? Or maybe you’re just looking for a new hobby project! Give it a go!
It’ll also be a great way to show off the awesome benefits of [[your-favorite-language-of-choice]] - look at you, Gophers and Rustaceans! Python - do you have it in you? Prove your language is the best for big data!
I really think that as data becomes bigger and bandwidth becomes more plentiful over the next 5, 10 and 20 years, that whatever Free software suite that fills this void will become as important as Apache, wget and BitTorrent are today. Be part of the future!
Let’s go!
So, are you interested? Shoot me an email at miserlou [at without parenthesis] gmail [dot without parenthesis] com! If there’s interest, I’ll put together a Slack or a mailing list or a GitHub project where we can discuss a plan of attack!
Let’s make big data Free again!
Too Long, Didn’t Read
tl;dr: 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!
A Big Data Transfer Protocol
For the past thirty years, the web’s HTTP protocol has been really great at serving things like web pages, chat messages, images, and other objects at the kilobyte to megabyte scale. Unfortunately, the web was not designed for the “big data” objects of today - genetic sequences, large databases, high definition media, and other files at the terabyte to petabyte scale. HTTP transfers over the open internet are hampered by constant connection re-establishment and TCP overhead. Some reconnection problems have been addressed in HTTP/2, but not the overall throughput issues.
The fact is, for very large files, HTTP is slow.
However, there is an alternative, proprietary protocol - FASP, the Fast and Secure Protocol - more known commonly by the client/server software product name Aspera, which avoids these problems. Aspera can deliver speeds up to 1000x times faster than HTTP/FTP. I honestly didn’t believe it until I saw it for myself. In fact, I had never even heard of Aspera before I started this job, and there wasn’t even an English-language Wikipedia article for FASP yet - although I’ve since written one.
Out of necessity, many organizations are now using this proprietary software for large data transfers, including public institutions such as the National Institute of Health, the European Genome Archive/Sequence Read Archive, the National Cancer Institute/cancer.gov, FEMA and private companies, such as Amazon, Netflix and the owner of Aspera, IBM. Basically, if you’re working at terabyte scale, you probably need this software.
Demonstration
Let me reproduce an experiment for you. We’re going to download an experiment’s worth of RNA-Seq expression data from the Sequence Read Archive, which offers both FTP and Aspera downloads. On the left is FTP with wget, which starts first, and on the right the Aspera client, ascp. This test was performed on two different EC2 instances in us-east-1, fetching a 343MB FASTQ file from the Sequence Read Archive, which is in the UK.
As you can see, the ASCP client performs over 200x faster than FTP, and can download the whole file in 9 seconds. It’s pretty magical.
It’s also necessary for our project’s basic feasibility. Without Aspera, it would take us months to years to download the millions of samples like this that we need to process. We’d have to fly all over the world with suitcases full of hard drives to be able to collect our data!
A Proprietary Protocol, a Free Software Solution
In theory, the protocol is simple-ish. The client establishes an SSH connection to the server for negotiating the control of data flow, and then a range of UDP ports above 33001, one for each connection thread, are used to transmit a unidirectional transfer of data, and requests for retransmission are sent back over the SSH connection.
I say in theory, however, because the software is proprietary. So, I have no way of knowing what the protocol is actually doing during a file transfer, just as I have no way of knowing what the client software is doing to my laptop, or what the server software is doing to my servers.
Aspera is owned by IBM - does their client spy on what else is running on my system and report it back to their headquarters as business intelligence? If asked, would they share this information with the government? Without the source code, it’s impossible to tell!
Those were things people used to worry about in the very early days of the internet, until the invention of the Apache web server, which, along with GNU/Linux, truly democratized the web and allowed the explosion of growth which we all benefitted from.
I think a Free Software implementation of Aspera, or something similar, will cause a similar revolution for big data.
Implications
There are obviously many immediate practical implications for having a Free FASP client/server/library implementation.
Science
Firstly, and most relevantly to our work at the Childhood Cancer Data Lab, biologists, physicists and other scientists who deal with “big data” won’t have to use proprietary software to retrieve and share the data they need in a timely fashion. That alone would be a massive boost for science, for software freedom and for data sharing everywhere. But the benefits don’t stop there!
Technology
There are also massive implications for system administrators and software developers. For example, many organizations have moved to using Docker images as part of their system deployments, and although the best practice is to have these images be as small as possible, in practice, this is rarely the case. Images can balloon up to be many tens or even hundreds of gigabytes, especially if they contain large machine learning models or training datasets.
How many thousands of hours of engineer time have already been wasted waiting for slow pulls from DockerHub? A switch to FASP could cut hours down into seconds.
Business
There are also large business implementations. Global businesses who need to share large amounts of data across different regions, especially if that data has to be transferred over the open internet, could massively benefit from radically faster transfers - and in fact, this is IBM/Aspera’s business model!
Filesharing
Although the nature of the protocol makes it difficult to use on some personal networks, I do think that elements of the technology could benefit consumer file-sharing, which has not had any major revolutions since the adoption of BitTorrent in the early 2000s - nearly 20 years ago! BitTorrent isn’t actually too dissimilar to Aspera, so maybe a free FASP implementation would end up replacing or amending file locker services like Mega, which serve massive files over HTTP - do you want to be the next Kim Dotcom? A detailed showdown of BitTorrent versus Aspera would also be really useful for understanding this problem space.
Publishing
Lastly, and definitely not least, I think this project could significantly benefit journalism and publishing.
We are entering the age of big data journalism, and I think the start of that era has been marked by the publishing of the Panama Papers, which was 2.7 terabytes of leaked information. Leaking that over HTTP/FTP upload could take weeks!
In the future, more and more investigative journalism will be driven by leaks of databases and the publishing of massive caches of documents. Currently, the best way that I know of to transfer 2.7TB is to send a bunch of external hard drives in the post. With better FASP Free infrastructure, that won’t be the case forever.
Approaching the Problem
I see two approaches to solving this problem - a reverse-engineering solution and a “clean room” solution. The FASP protocol is not publicly documented, and the technology itself is patented (with a misspelling in the patent title), which may scare off some of the usual suspects like Redhat or Google from developing this technology further.
So, it’s up to us hackers!
Reverse Engineering
The first approach would be to reverse engineer the protocol to create a Free client that can speak to existing servers. This would be immediately useful to us at the CCDL, as we’re not able to distribute proprietary software in our Docker images, so we have to re-run the Aspera installer for every server we instantiate, which costs us time and money.
From there, a server compatible with the Free client could be created and made to work in tandem with the Free client. This would then benefit us at the CCDL as well, as we want to share our massive dataset with other cancer researchers and machine learning researchers without having to use AWS S3’s HTTP methods.
Although this method is probably easier, and perhaps more immediately useful, it may make the lawyers nervous, which could hinder business adoption in the long term, and it also leaves the broader community without a Free protocol specification.
Clean-Room
An alternative approach would be to ignore the existing Aspera server and client implementations and to try to define a new transmission protocol which solves the same problem at the same level of performance without directly copying the methods.
This method will probably have a higher risk of overall project failure as the timeframe will be longer and the amount of cooperation required will be a lot higher, but the ultimate product would be better: a new, Free protocol and reference client/server implementations to power the future of big data file transfers. This way, we’re not limited by the restrictions of Aspera as it stands, and we can potentially add new features, such are parallel endpoints and content discovery.
It could be you!
Now, here’s the really exciting part: You could be the one to do it!
If you’re a great developer who loves free software but has never been a leader of a major Free software project, I strongly encourage you to try it! It won’t lead you to riches (outside of healthy consulting fees), but it can certainly lead you to awesome grant opportunities, chances to travel internationally for free to speak at conferences, lots of new friends, and it will greatly improve your programming, project management and team leadership skills. Give it a shot!
Maybe you’re working on a CS masters degree and are looking for a thesis project? Maybe your company uses Big Data and gives you 20% time to work on whatever you like? Or maybe you’re just looking for a new hobby project! Give it a go!
It’ll also be a great way to show off the awesome benefits of [[your-favorite-language-of-choice]] - look at you, Gophers and Rustaceans! Python - do you have it in you? Prove your language is the best for big data!
I really think that as data becomes bigger and bandwidth becomes more plentiful over the next 5, 10 and 20 years, that whatever Free software suite that fills this void will become as important as Apache, wget and BitTorrent are today. Be part of the future!
Let’s go!
So, are you interested? Shoot me an email at miserlou [at without parenthesis] gmail [dot without parenthesis] com! If there’s interest, I’ll put together a Slack or a mailing list or a GitHub project where we can discuss a plan of attack!
Let’s make big data Free again!
Related Post
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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.
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.
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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.
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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!
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.
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!
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).
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!
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!
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.
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.
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.
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.
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.
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!
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.
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.
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.
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!
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!
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.
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.
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.
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.
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.
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.
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!
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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!
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).
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
'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.
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.
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?
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.
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.
When the Data Lab launched the Single-cell Pediatric Cancer Atlas (ScPCA) Portal in 2022, we knew it was only the beginning! We started by making data easily available for the research community and received an overwhelmingly positive response. But we know firsthand from training hundreds of pediatric cancer researchers in analysis that making data available is just the first step. We’re increasing the impact of the Portal by listening to the growing ScPCA community. Now more researchers can contribute datasets, new features are continuously being developed, and we started an open, collaborative project to further explore the available data! Here’s a look back at how we’ve enhanced the ScPCA Portal in 2024.
Launching the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project in April 2024 was a highlight of our year! This community-driven initiative aims to analyze data from the ScPCA Portal, which currently holds 700 samples from over 55 pediatric cancer types. The project is a step forward in advancing our knowledge of pediatric cancers through single-cell analysis, and we're excited to expand OpenScPCA in 2025! To that end, we're reflecting on some of our recent accomplishments and how we can keep that momentum going into next year.
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