New DSL "MassQL" lets scientists query mass spectrometry data
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Re: New DSL "MassQL" lets scientists query mass spectrometry data
#2I’m curious how this compares to traditional tools (like scripting in Python/R) for analyzing such datasets, both in ease of use and performance. Also, could similar query languages be developed for other fields (genomics, imaging, etc.) to empower domain experts? It’s cool to see a new DSL in academia
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#3This is an anti-pattern. Do not make DSLs for subdomains of science. All scientific data can be stored and queried using general-purpose data analysis tools.
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#4This is an anti-pattern. Do not make DSLs for subdomains of science. All scientific data can be stored and queried using general-purpose data analysis tools.
Why not if it is to facilitate new discoveries and to extend the reach of computational tools to large swaths of clever and productive people?
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#5This is an anti-pattern. Do not make DSLs for subdomains of science. All scientific data can be stored and queried using general-purpose data analysis tools.
Why not if it is to facilitate new discoveries and to extend the reach of computational tools to large swaths of clever and productive people?
because sql and other well-established systems already do this and tools like this can be built on those systems without creating yet another domain-specific tool.
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#6MassQL Introduction: https://mwang87.github.io/MassQueryLanguage_Documentation/
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#7Earlier quoted context omitted.
Why not if it is to facilitate new discoveries and to extend the reach of computational tools to large swaths of clever and productive people?
because sql and other well-established systems already do this and tools like this can be built on those systems without creating yet another domain-specific tool.
Like this group has a set of modules locked in a specialization using this DSL https://en.wikipedia.org/wiki/Nextflow
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#8Was not familiar with the details of mass spectography.
Found this[1] page which includes an explanation of how it works, and also shows some analysis using the Spectra R package.
The SpectraQL[2] package adds MassQL support to Spectra, so one can compare a bit.
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#9This is an anti-pattern. Do not make DSLs for subdomains of science. All scientific data can be stored and queried using general-purpose data analysis tools.
Is there no need to engage with the content at all to make this judgment? Just, DSL bad? Always and everywhere?
Re: New DSL "MassQL" lets scientists query mass spectrometry data
#10This is an anti-pattern. Do not make DSLs for subdomains of science. All scientific data can be stored and queried using general-purpose data analysis tools.
The point of tools is to let us do things. In the end we don’t get a pat on the back for using one language instead of another. What we need is tools to do our actual work, which is not software engineering. If that tool is a DSL, then so be it.
General-purpose data analysis tools tend not to be well suited to most types of scientific data. And it’s not only mass spectrometry, but also microscopy, diffraction, etc. There are huge improvements to be made in these areas.