Red-eying it to Boston to get some exciting projects started at Ginkgo this week. Lots of meetings and lots of design decisions to make in a very short amount of time.
Anthony Barente
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Bioinformaticist interested in #Proteomics, #Genomics, and #DataScience. Currently building software for #SyntheticBiology at Ginkgo Bioworks.
Another periodic reminder that multiprocessing.cpu_count() will not give you the correct number of vCPUs on AWS batch. It returns the CPU count of the machine, even if you can't use all the cores.
naturepoker"An assembly is a hypothesis of the genome" something I try to keep in mind through all this.
Carl T. BergstromCochrane Reviews has issued an editor's statement about the mask-wearing paper that has been getting so much attention lately.
Below, the statement, in which they both endeavor to clarify the implications of the study and take responsibility for the poor initial job of public communication.
Eli Roberson (he/him)I understand that micromamba is supposed to be faster than conda. But I didn't know it was SO much faster.
Ellen L. SimmsCBC’s “Marketplace” is doing some fascinating reporting on DNA tests. The articles are entertaining, and provide a bit of education on why the results are so unpredictable and unreliable.
Dogs: https://www.cbc.ca/news/business/marketplace-dog-dna-test-1.6763274
Humans:
https://www.cbc.ca/news/science/dna-ancestry-kits-twins-marketplace-1.4980976
We can and still do enforce schemas though. We've just moved this logic out of the main database and the API that serves it.
Dave TangMy 300th blog post where I write about customising BLAST output https://davetang.org/muse/2023/02/15/til-that-you-can-customise-blast-output/
TIL that you can customise BLAST output - Dave Tang's blog
I am going to start a new series of posts based on new things (new to me) I learned about recently and they will be included in the TIL category. I learned about TIL from the bird app a while ago and it is based on the popular subreddit todayilearned. I used to post TIL...
An interesting conundrum about dealing with data in a company with so many different types of biological teams and experiments is satisfying domain specific needs with very general database infrastructure.
We have a relational database and the models, like Sample, have a well defined meaning. But if a team wants a Tissue Sample, now I have to specify a set of properties to store for each Sample to make it a new "type", e.g organ.
Generality is awesome but sometimes kinda messy.
Marc Robinson-RechaviNew preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
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https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
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