- Who are we and what do we bring to the table?
- What problems are eligible for this platform?
- What should I keep in mind before uploading my data?
- How to upload data?
- I am a life scientist / clinical professional …
- I am a data scientist…
- Discourse Guidelines
We are a community of data scientists and medical professionals / life scientists on a shared quest to defeat COVID-19.
Are you a medical professional / biochemist / virologist / infectious disease specialist / drug developer / … and:
have a dataset and want us to help you extract insights?
have to wrestle with spreadsheets and / or execute tedious but monotonous tasks?
have data of any modality but no time and resources to process them at scale?
have learned of an existing model that you would like to use, but do not have the time or technical expertise to run them on your data?
looking for a specialized tool tailored to your specific needs?
We invite you to use our community to solicit the service of dedicated volunteer data scientists and bioinformaticians from around the world. To get started, simply ask us a question.
We are exclusively committed to working on problems that help mitigate / find a cure or vaccine against COVID-19, on a timescale from weeks to months. When uploading data and / or questions, you do not need to justify your request; but you do pledge that your work serves the above purpose.
You bear the moral and legal responsibility for any data that you upload. To take an example, when you upload microscopy images, there will in most cases be no concerns whatsoever (as long as you don’t put the name of a patient in the file name or metadata). However, when uploading data that may allow the deduction of the identity of a patient, then let’s first work on anonymizing that data properly before you upload it. Please head to the category “Anonymization” and allow us to work on anonymization with you on secure channels before you upload your data and make it visible to the world at large.
We recommend using Zenodo.org or figshare to make the data available. You may also use Google Drive, Dropbox and the likes. In any case, please respect legal requirements and seek our help with anonymization, if needed.
If possible, please let us know in what form, shape, or structure you would like to receive analysis results (you might for example want or need to further process the data with existing tools). Also, please let us know if you need results prior to a given deadline.
That said, it is okay to not know what results to expect at the outset, in which case we (data scientists) will extract information and insights in accordance with our expertise and experience.
We encourage you to share your data as openly as possible (after ensuring that any privacy concerns are resolved) to make fast progress. We suggest you use CC BY-SA. For further information on licenses see e.g. this guide.
You are here to help the common good. Your service is invaluable and yet there is no monetary compensation involved. We all work here for free, to beat the pandemic as soon as possible.
In most cases, you will be asked to supply merely an analysis result, not a software pipeline. However, your result should be reproducible, so please accompany it by a pointer to an open source repository such as github.com whenever possible to allow others to verify and build upon your result.
If you are asked to provide software: please make your solution as easy to use and execute as possible. Time is precious, and we cannot expect medical professionals to set up complex software pipelines or be concerned with resolving complex dependencies.
The most efficient way to solve some one-off tasks might be to do them manually. Please refer to our “citizen science” department in that case.
If you are working on a complex task that takes longer, use the forum to give intermediate updates.
Any numerical or pictorial results of computations posted in this forum have to follow the BSD license. We encourage you to also use similarly open licenses for any code you provide in order to easily enable others to build on it.
Be Agreeable , Even When You Disagree.
You may wish to respond to something by disagreeing with it. That’s fine. But, remember to criticize ideas, not people.
You may not post anything digital that belongs to someone else without permission. You may not post descriptions of, links to, or methods for stealing someone’s intellectual property (software, video, audio, images), or for breaking any other law.
Yes, legalese is boring, but we must protect ourselves – and by extension, you and your data – against unfriendly folks. We have a Terms of Service describing your (and our) behavior and rights related to content, privacy, and laws. To use this service, you must agree to abide by our TOS.