How much bioinformatics at your DIY lab?

[Patrik D'haeseleer]

Hoping for some quick feedback - How much use to people at your community lab make of bioinformatics? What is the most sophisticated piece of computational work you've done so far? 

At Counter Culture Labs, we have someone doing molecular dynamics simulations for protein linker design. And at BioCurious, we mined some Arabidopsis gene expression data to design novel spatiotemporal promoters. That's about the most sophisticated we've done so far. Other than that, it's mostly some Blast, primer design, codon optimization etc - nothing fancy.

I've been asked to be on a National Academy of Sciences panel this Thursday about synbio and DIYbio (together with Drew Endy, and Tom Burkett from BUGSS), and I'm supposed to talk about how computational tools are enhancing ease of use in DIY labs. Figured I'd do a quick poll of the rest of the community...

Thanks!

Patrik

[djwr...@gmail.com]

At Thel4b we compared toxo Gondi genes to human genes using blast and discovered toxo Gondi codes for dopamine precursors.  Stanford published this a couple of months after our project which was designed to familiarize a beginner like me with blast.

Dan

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[Jason Bobe]

Looking ahead, I think Jupyter notebooks hold tremendous potential for enable new wave of learning and discovery:

http://jupyter.org/

I'm hoping to use this for workshops on resilience algorithms in next year.

Jason

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[Abizar Lakdawalla]

I use Galaxy ...

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[Cory Tobin]

In addition to what Dan said, at TheLab most of the bioinformatics if you want to call it that is just folks using Snapgene to plan out molecular cloning activities.  On a few occasions I have tried to get group bioinformatics projects going but they tend to fizzle out quickly.

There's a lot of low-hanging fruit and I think community labs have the ability to tackle some grand problems. But I have found organization and communication to be the largest hindrance to progress. A small group of people who speak the same technical lingo can make quick progress but once you have a large group with varying education backgrounds, we spend so much time laying out the basics that the more advanced folks get bored and disperse and the project quietly dies.

The most advanced thing we've done is assemble a bacteria genome combining Illumina short reads, PacBio long reads and optical mapping data to put together a mostly complete draft chromosome.

-Cory

[Björn Johansson]

Check out cloning in Jupyter notebooks with pydna.

This is a new way to document genetic constructs that should be useful for sharing cloning constructs online.

(Disclaimer I am the developer of pydna).

[Brendan Desmond]

I'm interested in coming up with beginner to intermediate-level
bioinformatics projects for my local DIY bio group. I think I'm okay
with figuring out what tools to use, but I'm a bit fuzzy on where to
find data to play with. With regards to the "Illumina short reads,
PacBio long reads, and optical mapping data", did you obtain all of this
data yourself first-hand from your own samples? If not, where might one
look to find freely available data to experiment with?

-Brendan

[Tom Randall]

The most sophisticated is using standard assemble to reference tools within Galaxy for a fungal genome that I had MWG Operon sequence for me on an Illumina HiSeq machine. See about halfway down this page for a brief description.
http://roningenetics.org/Sequencing.html

Tom

[Sebastian Cocioba]

Doing whole genome sequencing on a plant. Used nanopore reads and currently assembling plastid genomes and then will use Amazon AWS to do the nuclear assembly. Largest computational project Ive done thus far. Bioinformatics has become the cornerstone of my research effects in my home lab. 

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[John Griessen]

On 05/29/2017 11:55 AM, Sebastian Cocioba wrote:
> Doing whole genome sequencing on a plant. Used nanopore reads and currently assembling plastid genomes and then will use Amazon
> AWS to do the nuclear assembly. Largest computational project Ive done thus far. Bioinformatics has become the cornerstone of my
> research effects in my home lab.

Sounds close to GMO time. Will you be trying DNA that has some errors from reads and assembly, and do you have any redundant
DNA in there to offset errors?