Re: [DIYbio] Re: Volunteering in Bioinformatics

Hey William,

Pysplicer has code that does this, but not as a standalone task. That is, it allows one to exclude arbitrary IUPAC-notation sequences, as well as high gibbs-free-energy structures, from RNA and DNA during CDS optimisation. However, it only does this *while* CDS optimising rather than upon a preexisting CDS. So, you could dig in there and rip that out?

https://github.com/cathalgarvey/pysplicer

I have begun, tentatively, a Go rewrite to implement PySplicer as an Antha module.

On 27 February 2016 02:05:02 GMT+00:00, William Beeson <bees...@gmail.com> wrote:

David,

I am working on a program (perl) that automatically finds and removes type II restriction sites from fungal genomic DNA by making silent mutations in CDS or single mutations in regulatory elements.  The end goal of the program is to automatically generate a series of primers and a task list so that you can convert any fungal gene (from genomic DNA) to golden gate compatible.  I've got most of the logic worked out, but there are some complicated challenges with doing this efficiently.  If you wanted to help with that send me an email.  

-Will

PS: If anyone knows of a similar program that is published somewhere that I can build off of I would appreciate it as well.  I have had to make this from scratch thus far.

On Thursday, February 25, 2016 at 7:03:21 PM UTC-5, David Zehnter wrote:

I've spent a lot of spare time studying biomedical concepts like (epi)genetics, molecular biology, disease genotypes and phenotypes, etc. As a volunteer for a neurogenetic research group I have participated on an exome analysis pipeline (variant calling and annotation). I have a modest understanding of statistics and machine learning, I'm into it. I work 30 hours a week as a Node.js and Python developer for a small company that has nothing to do with bioinformatics. Node.js seems to become popular for bioinformatics, there are many projects now. And I love Python! I'm a DIYbio believer with a strong autodidact and non-academic attitude. I'm currently looking for a new volunteering project. If you are a bioinformatician who could need some extra support, please get in touch with me. I'm willing to spend about 10-20 hours a week to help you getting results while you guide me (not teach me) and well, be a kind of supervisor. It could be anything related to research, software development, web apps .. whatever. Anyone with similar experience? I found this article motivating. Please share, thanks!

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