Automa.jl
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Automa.jl | svls | |
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2 | 3 | |
176 | 411 | |
1.1% | - | |
7.0 | 8.1 | |
4 months ago | 6 days ago | |
Julia | Rust | |
GNU General Public License v3.0 or later | MIT License |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Automa.jl
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Julia Receives DARPA Award to Accelerate Electronics Simulation by 1,000x
You don't need to have any particular skills except familiarity with Julia, but it's obviously an advantage to have a bio background - depending on what you're going to do.
Usually, the best packages come about when people are motivated to creating something specific, for example if they think the status quo in some domain is not good enough.
I'm sure we can dig up a handful of old, badly maintained projects that could use some love. Off the top of my head, it would be nice to have
* Micro-optimized our smith-waterman algorithm. That's probably fairly easy to get started with if you're not a bio person
* A number of our parsers have not been properly maintained. We use finite state automata https://github.com/BioJulia/Automa.jl to create parsers. That's for more advanced users
Feel free to get in touch on the Julia Slack, or send me an email :)
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Ask HN: How to Get Started with Julia?
I'm not in bioinformatics and don't do string processing, so I can't really help too much here.
I'd really urge you to come ask this on the julia Discourse Forum or Zulip and I promise you'll get high quality useful responses from people who understand your needs better than I.
> How do I find substrings & replace them efficiently? How do you split a string with delimiters? Regular Expressions?
This is something that the BioJulia people have put a lot of work into. Yes, you can use regular expressions, but they've managed to squeeze a lot of performance out of more specialized approaches, e.g.
https://github.com/BioJulia/Automa.jl
https://github.com/jakobnissen/ScanByte.jl
But for more straightforward usage, julia has the `findfirst` function which can search for occurrences of a substring, `replace` which can do replacements either with a literal pattern or a regex, and `split` which can split a string with delimiters.
svls
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How to configure vim like an IDE
svls
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svls VS verible - a user suggested alternative
2 projects | 3 Nov 2021
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Julia Receives DARPA Award to Accelerate Electronics Simulation by 1,000x
I can attest first-hand to the "headache" that comes from semi company simulation environments. Not only are they horribly outdated (in Perl/Tcl), but they're different at every company you work at. There's no gold standard because the standard that these EDA companies ought to be making doesn't exist.
There needs to be an open initiative between semi companies to create a standard simulation environment -- with compilers, unit-test frameworks, and all sorts of simulation (gate-level, analog/mixed signal, emulation, etc). Hell, just give me a free IDE plugin for SystemVerilog that actually works.
This lack of a standard seems to me like the critical path in hardware design. I'm trying to support projects to fix this like SVLS (A language server for SystemVerilog: https://github.com/dalance/svls) but these are all hard problems to solve. This industry is relatively niche and doesn't seem to have many engineers interested in FOSS.
What are some alternatives?
Octavian.jl - Multi-threaded BLAS-like library that provides pure Julia matrix multiplication
verible - Verible is a suite of SystemVerilog developer tools, including a parser, style-linter, formatter and language server