Soliciting the help of the Bioinformatics Community

prussiap · 05-25-2012, 02:52 PM

Hello Everyone,
I'm a geneticist and I've predominantly worked with miRNAs and am now switching to the analysis steps. I'm talking about RNA-seq analysis here.

As bioinformaticians or geneticists if you could give direction to some programmers, who had no background in genetics, what problems would you want them to tackle? What pain and slow-down do you have in your daily activities? What needs optimising, what needs gluing, what needs coding?Especially interested in problems that can be gamified for people e.g. phylo.

The goal for us is to find a problem that computers can't do so well and to optimize it with human pattern matching.

severin · 05-27-2012, 04:20 AM

We have great tools to get us to a draft assembly but there are still quite a few areas of the genome that the automatic assemblers just can't handle. If there was a visualization tool that would allow researchers/individuals to look at the scaffolds in a draft assembly and then use evidence to indicate yes these two should be joined into a superscaffold and these 10 into a chromosome etc.

I have long thought that we are addicted to this instant gratification of bioinformatics analysis when in reality there are many tasks that are done better using the visual cortex, a well designed GUI, and a few months.

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05-25-2012, 02:52 PM	#1
prussiap Junior Member Location: 94608 Join Date: May 2012 Posts: 6	Soliciting the help of the Bioinformatics Community Hello Everyone, I'm a geneticist and I've predominantly worked with miRNAs and am now switching to the analysis steps. I'm talking about RNA-seq analysis here. As bioinformaticians or geneticists if you could give direction to some programmers, who had no background in genetics, what problems would you want them to tackle? What pain and slow-down do you have in your daily activities? What needs optimising, what needs gluing, what needs coding?Especially interested in problems that can be gamified for people e.g. phylo. The goal for us is to find a problem that computers can't do so well and to optimize it with human pattern matching.

05-27-2012, 04:20 AM	#2
severin Genome Informatics Facility Location: Iowa @isugif Join Date: Sep 2009 Posts: 105	manual genome assembly We have great tools to get us to a draft assembly but there are still quite a few areas of the genome that the automatic assemblers just can't handle. If there was a visualization tool that would allow researchers/individuals to look at the scaffolds in a draft assembly and then use evidence to indicate yes these two should be joined into a superscaffold and these 10 into a chromosome etc. I have long thought that we are addicted to this instant gratification of bioinformatics analysis when in reality there are many tasks that are done better using the visual cortex, a well designed GUI, and a few months.