Chan Zuckerberg Initiative hit a home run

Maintaining bioinformatics infrastructures is really challenging with the current Grant schemes. Most of the time what you have ahead for your software are the following plans: bug fixing, documentation, user support, refactoring to make the software faster or compatible with different platforms or architectures... This is almost impossible to be sold by itself in a grant proposal. It needs to be blur or hidden in the proposal with new improvements, data support or data analysis.. probably with new ideas that the developer and the PI don't even try before. But still, you need to get the grant. 

In summary, the bioinformatics community is struggling to get money to maintain and support bioinformatics software and databases. Different initiatives and grant calls have been created in recent years to support and sustain the bioinformatics open-source community. But, they have encouraged the creation of "new/novel" things rather than support the development of well-established tools. And here, is when Mark and the Chan Zuckerberg Initiative succeed today.

The Chan Zuckerberg Initiative (CZI) announced the final list of bioinformatics open-source projects awarded with the CZI’s Grant. After reading the final list, it was clear to me that this group of reviewers really knows what they are doing and the CZI is really pushing forward to maintain bioinformatics infrastructures and software.




Let's have a look at some of the projects: 

Plotly combined the power of scikit-image and Dash to a larger number of scientists thanks to increased execution speed, interactive image annotation, and processing.

 

Here, a quick look at the number of Fork, Pull Requests, and use of the library in Github (parameters that should be used to measure the real impact of an open-source project).

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Bioconductor Build System: Continuous Integration and Developer Feedback. To reengineer the Bioconductor build system for nightly continuous integration, production, and distribution of tarballs and binaries for over 1,700 user-contributed software packages.

If you are in Bioinformatics, you know Bioconductor, period. Well, CZI is given money to Bioconductor to refactoring the CI/CD system

this is really amazing. This is.. developers understanding what developers need. 

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BioConda:  To establish teaching material, improve documentation, and minimize the maintenance effort of the Bioconda project by extending automation of code review, testing, and building.



BioConda is a new and emerging bioinformatics community (if you haven't used it, read here about it).

Just to have a look at the community engage, see this GitHub statistics, more than 800 contributors, 20k commits and amazing integration with other platforms like BioContainers.

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Matplotlib: To enable Matplotlib to continue as the core plotting library of the scientific Python ecosystem by addressing the maintenance backlog and planning Matplotlib's evolution to meet the community’s visualization challenges for the next decade.

Check this out, use by 143K 

In total, these tools summarize more than 35000 citations (for those Who like citations). The complete list can be found here and it includes Cytoscape, GATK, etc.

But before finishing and congratulate CZI and Mark's initiative, here are two examples that make clear this committee really knows what they were doing... and the examples, of course, are in the field of Proteomics and Mass spectrometry.

MSstats by Olga Vitek and Meena Choi; and OpenMS by Hannes and Timo. For those who read my blog posts and follow me on twitter is not new that I advocate for Open-source and community efforts in the field of proteomics all my career (see this long review). It is a well-known problem that proteomics and mass spectrometry is dominated by commercial or closed-source projects. I have been teaching at EBI OpenMS for two years and I know how amazing, well supported and versatile is the framework (see some lectures). The nomination (from my point of view) of these two leading projects in the field, is also an award regarding their efforts to promote open-source in the proteomics and mass spectrometry community. 

Thanks to CZI.