Volunteering in Bioinformatics

[David Zehnter]

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!

[Xabier Vázquez Campos]

In GitHub there is a large bioinformatics community, many of the tools are in continuous improvement, at least if they are recent, and they are usually open to add functional scripts made by anyone if that improves the functionality of their software, or to fixing code.

You can also ask in Biostar, Seqanswers and Twitter. I'm using bioinformatics continuously (microbial ecology, metagenomics...) but I have no coding skills further than simple bash scripting. I know that the Australian Centre of Ecogenomics has in development several tools collectively known as "M suite", e.g. GraftM, and the Huttenhower Lab also have many in active development in their biobakery.

Good luck

[Ravasz]

Hi David,

What kind of project would you be interested in? Also, do you have a github page or something alike that shows what type of programs you like to write?
I always have a few unused bioinformatic projects up my sleeve for students. My focus is on proteomics and RNA sequencing of T cells. If you are interested in this, let me know. I am a biologist first, and tend to dabble with coding (python and R) and for more complex code I could often use some proper programming support.

Mate

[William Beeson]

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.

[David Zehnter]

I was doing some tests with ANNOVAR and SeqMule, therefore created a few Python scripts to filter .csv files. I've done some NLP and biomedical text mining/ontologies. I played around with graphs using Cytoscape and Gephi. I'm currently working on a webapp with node.js for my company and do some research on node.js + distributed computing and CDNs. I would be very interested into proteomic networks, epigenetic regulatory networks, transcriptomics, etc! I really like graphs, could this be helpfull? Just let me know something you need and I'll try on it. Just created a github where I will upload things related to bioinformatics.

[Cathal (Phone)]

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.

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

[William Beeson]

Hi Cathal,

I looked at the description and don't think it quite matches what I'm trying to do.  I am not trying to codon optimize a sequence so that I can then order the gene from a synthesis company.  I am trying to make a general software that will take existing genomic DNA and tell me how to remove unwanted type II restriction sites and reassemble the gene without those sites using PCR.  I will show an example of what I am trying to do later on so that it is more clear.  Doing this manually is very tedious and time consuming.

-Will