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What does "first language tailored specifically to bioinformatics" mean? I ask because I'm pretty sure there have been earlier languages for bioinformatics. Ju

• mhenders 7y ago
  Love your bio, and those are some cool links. To your first question, seeing that in context of their paper abstract, I think the emphasis should be on the last part of the sentence, "...which marries the ease and productivity of Python with C-like performance."
  • dalke 7y ago
    There's a comma before that clause, which suggests that it's not meant to be interpreted as "the first bioinformatics-specific programming language to marry C and Python" but rather as "the first bioinformatics-specific programming language (oh, and it marries C and Python)." Which bio? My most recently updated one is http://mmpdb.dalkescientific.com/about.html http://mmpdb.dalkescientific.com/about.html .
    • mhenders 7y ago
      http://www.dalkescientific.com/company.html http://www.dalkescientific.com/company.html Boy, what a body of work. Would love to hear your take on Seq if you get a chance to dig in more. I come from more of a Python background and really like what I see: - Python syntax for the most part - Mypy style type annotations - |> for pipelining and ||> to parallelize - match constructs (ML-ish with guards) - s'ACGT' and k'ACGT' for sequences and k-mers It's relatively early in the project but I think the choices they have made give them a chance to continue to build momentum.
      • dalke 7y ago
        Thanks for the pointer. And praise. I have several bios out there, for different purposes. I should update that one .... and the web site. Been meaning to do that for a long time. sigh I don't have the interest to evaluate Seq. I only did bioinformatics for a couple of years, and that was almost 20 years ago. I am incapable of giving it a serious look. My cursory look is that it's only really meant for DNA, and highly optimized for the specific k-mer benchmark compared. My personal opinion is that developing a new programming language is a hard and almost thankless task. Yet they are also so very fun to do. Back in the 1980s and 1990s, a number of computational life sciences packages (eg, Sybyl Programming Language (SPL) from Tripos, X-PLOR, Scientific Vector Language (SVL) from CCG) developed their own domain specific languages. They were successful (IMO) more because of the tools available through them than the language themselves. In the early 1990s I started work on VMD. We had a simple scripting language. As one did back then. I found that Tcl was similar, embeddable, more powerful, and cleaner than anything we did, so we switched to that. As a result, we got a lot of things "for free", like easy access to third-party packages designed for Tcl, and the faster bytecode engine from Tcl 8. I switched to using Python full-time in the late 1990s, and again saw just how much I got "for free" by using a language designed by people with software language design and implementation expertise, and with the vast set of support packages. Seq also gets some things "for free" because it builds on LLVM. But since it's completely independent of the CPython run-time and garbage collection model, it's impossible to build on any of the existing modules.
    • dalke 7y ago
• jerven 7y ago
  There is Darwin from the 90's https://inf.ethz.ch/personal/gonnet/DarwinManual/ https://inf.ethz.ch/personal/gonnet/DarwinManual/
  • dalke 7y ago
    Thank you! I remembered a group in Europe developed a language, but I couldn't remember the name - that was it!
• dalke 7y ago
  FWIW, SARVAVID is mentioned in the "Related Work" but "it lacks generality". And "Biopython" is misspelled as "BioPython." A common mistake.