Soliciting the help of the Bioinformatics Community

[prussiap]

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]

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.

[prussiap]

Hi,
That seems like an interesting start for our model. Do you have specific tools/methods in mind to improve this? How is the draft genome assembled currently ?

Yes our plan is to get humans to pattern match for us to improve a process or analysis. This might be a good example to use.

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.

[prussiap]

Hi,
Thanks for the answer. How is the draft assembly currently made? Our idea is to use human pattern matching to match the "outliers". Could you point me to some articles if any that describe this process?

I'd be willing to find out more to see if we could fit this in our platform

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.