Automa.jl VS Verilog.jl

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 :)

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.

It doesn't have to be. I once made a julia->verilog transpiler that even recompiled your julia functions with verilator, so you could verify that the code was correct.

https://github.com/interplanetary-robot/Verilog.jl

Of course, gaining traction on something like this is tricky.

I actually think Erlang/BEAM would be a great choice for making EDA tools, because it has concurrent execution model that you could probably very easily make play nice in rudimentary simulations of circuits that have triggers (`always @` sort of stuff.

A long long long time ago, I wrote this (currently very unmaintained) julia project, don't know if this is useful to you, but it's pretty clear that there is a LOT of potential for julia in this domain: https://github.com/interplanetary-robot/Verilog.jl