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Seq – A programming language for computational genomics and bioinformatics

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Re: Seq – A programming language for computational genomics and bioinformatics

#31

Post by travisgriggs »

clusterhacks wrote: post #24

I am a CS person who works with bioinformaticians every day as part of my job. I really like that Seq seems to have built-in some parallelization ability. I spend no small amount of time in my day job doing that manually in R with RcppParallel for loops that are totally independent across each iteration. Bioinformaticians are often educated to use a specific programming language and environment. They aren't usually l…

So basically, the same thing that kept(keeps?) Visual Basic in use for so long.

My son works in polysci analytics and I see the same thing you describe. A group will pick a tool and flog all problems with it. Change rarely occurs. He was in the Stata camp at one university, the TidyVerse at MIT.

It’s very weird for me, I develop and maintain a piece of software that that has 3 OSes, and 5 languages to wrestle with as well as multiple “tool” technologies like Ansible/MQTT, etc. so I’m very much in a polyglot-best-tool-for-the-job environment. Observationally from a casual POV, I see pros/cons both ways.

Re: Seq – A programming language for computational genomics and bioinformatics

#33

Post by psychometry »

clusterhacks wrote: post #24

I am a CS person who works with bioinformaticians every day as part of my job. I really like that Seq seems to have built-in some parallelization ability. I spend no small amount of time in my day job doing that manually in R with RcppParallel for loops that are totally independent across each iteration. Bioinformaticians are often educated to use a specific programming language and environment. They aren't usually l…

Scientists like using R instead of because the language lets them get set up and coding quickly with RStudio. More importantly, the language, tooling, and ecosystem is very forgiving when it comes to code quality and style. There is good R code out there, but the R community generally lacks the wide acceptance of good coding practices you see with Python users: unit tests, sane dependency management, type hints, documentation, safe namespacing, etc.

It's really saying something when scientists think writing Python code is a pain, because Python's a pretty forgiving language, too.

Re: Seq – A programming language for computational genomics and bioinformatics

#34

Post by arshajii »

Hi everyone, I’m one of the developers on the Seq project — I was delighted to see it posted here! We started this project with a focus on bioinformatics, but since then we’ve added a lot of language features/libraries that have closed the gap with Python by a decent margin, and Seq today can be useful in other areas or even for general Python programs (although there are still limitations of course). We’re in the process of creating an extensible / plugin-able Python compiler based on Seq that allow for other domain-extensions. The upcoming release also has some neat features like OpenMP integration (e.g. “@par(num_threads=10) for i in range(N): …” will run the loop with 10 threads). Happy to answer any questions!

Re: Seq – A programming language for computational genomics and bioinformatics

#35

Post by arshajii »

chmaynard wrote: post #5

I'm wondering if Seq can also serve as a general-purpose replacement for Python whenever a fast executable is needed.

(I'm one of the developers on Seq.) We've actually been working mostly on closing the gap with Python for the last year or so. Seq can be useful for plain Python programs as well -- I give a bit more context in my comment above.

Re: Seq – A programming language for computational genomics and bioinformatics

#36

Post by adgjlsfhk1 »

arshajii wrote: post #34

Hi everyone, I’m one of the developers on the Seq project — I was delighted to see it posted here! We started this project with a focus on bioinformatics, but since then we’ve added a lot of language features/libraries that have closed the gap with Python by a decent margin, and Seq today can be useful in other areas or even for general Python programs (although there are still limitations of course). We’re in the pr…

Have follow-up benchmarks vs BioJulia been done since 2019? If I remember correctly at the time, the result was that BioJulia was faster once you consider that it did validation.

Re: Seq – A programming language for computational genomics and bioinformatics

#37

Post by arshajii »

adgjlsfhk1 wrote: post #36
arshajii wrote: post #34

Hi everyone, I’m one of the developers on the Seq project — I was delighted to see it posted here! We started this project with a focus on bioinformatics, but since then we’ve added a lot of language features/libraries that have closed the gap with Python by a decent margin, and Seq today can be useful in other areas or even for general Python programs (although there are still limitations of course). We’re in the pr…

Have follow-up benchmarks vs BioJulia been done since 2019? If I remember correctly at the time, the result was that BioJulia was faster once you consider that it did validation.

We haven't done too many comparisons with BioJulia since that paper, although we did address the (valid) issues they raised such as data validation (i.e. Seq now validates input data by default, but this can be optionally disabled). We did compare against them in our last paper in a sequence alignment benchmark: https://www.nature.com/articles/s41587-021-00985-6 (check the supplement).

Re: Seq – A programming language for computational genomics and bioinformatics

#38

Post by lf-non »

pietroppeter wrote: post #23
jpxw wrote: post #17

Earlier quoted context omitted.

I know nothing about Nim or genomics. Why is it odd that they didn’t include Nim?

Nim has had some success in genomics mainly thanks to the work of https://github.com/brentp Nim can be sold as a "A strongly-typed and statically-compiled high-performance Pythonic language" as Seq (although it is more than that and does not actually have as a goal to be Pythonic, see https://nim-lang.org/ or https://github.com/Araq/nimconf2021/blob/main/zennim.rst ). Still, given the small size of Nim community and…

Nim is not really 'pythonic'. It does have some superficial similarity with Python (being whitespace sensitive) but it begins to diverge pretty soon. This is not really a criticism of Nim. I quite like many of the choices in Nim.

Seq claims that vast majority of python programs would work as is. I have not validated that claim, but Nim can absolutely not make that claim. Any python library would require substantial porting effort to be translated to nim.

Re: Seq – A programming language for computational genomics and bioinformatics

#40

Post by Zababa »

pietroppeter wrote: post #23
jpxw wrote: post #17

Earlier quoted context omitted.

I know nothing about Nim or genomics. Why is it odd that they didn’t include Nim?

Nim has had some success in genomics mainly thanks to the work of https://github.com/brentp Nim can be sold as a "A strongly-typed and statically-compiled high-performance Pythonic language" as Seq (although it is more than that and does not actually have as a goal to be Pythonic, see https://nim-lang.org/ or https://github.com/Araq/nimconf2021/blob/main/zennim.rst ). Still, given the small size of Nim community and…

Calling Nim Python is like calling OCaml or Scala Python, it's not really true. The main reason people use Python is because it is Python, not because of an extractable list of things.
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