User: syntax

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syntax30
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30
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New User
Location:
Boston
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2 months, 2 weeks ago
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1 year, 4 months ago
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Posts by syntax

<prev • 7 results • page 1 of 1 • next >
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PubSub or workflows or both?
... I am building a chemistry application with django that focuses on reactions. It bonds an atom to an existing molecule. The reaction **event** triggers a bunch of (a) **validations** to make sure the feasibility of the molecule checks out (b) **subsequent events** as the molecule --- **Nested Funct ...
pubsub python workflow events written 3 months ago by syntax30
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Comment: A: Creating workflows with snakemake and conda
... Hmm. So I suppose this is great for running many different linear workflows on your local machine. But if you wanted to put a workflow system (that supports parallel execution and containers) into production on a cluster - what would you use? ...
written 3 months ago by syntax30
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Does vcf spec indicate cnv duplication of snps?
... Does the VCF spec have any way of indicating if a particular SNP is being duplicated due to CNV? Perhaps in the pipe delimited columns? ...
vcf ngs cnv snp snv written 8 months ago by syntax30
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Comment: C: Workflows! Where is the code?
... That seems to be the key distinction that i am failing to grasp. So in the workflow step's `config` it would define a *pre-determined tool to be run* on the input specified in the `process`? ...
written 10 months ago by syntax30
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Workflows! Where is the code?
... Hey there. Trying to wrap my head around workflows. Taking a look at the examples below, I don't see any Python/ R/ Java/ C/ PERL code - which is confusing as a developer that has entered bioinformatics. > *CWL* -- https://github.com/Duke-GCB/GGR-cwl/blob/master/v1.0/ChIP-seq_pipeline/01-qc-p ...
cwl workflows wdl written 10 months ago by syntax30 • updated 10 months ago by Michael R. Crusoe1.2k
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Encrypting BAM files
... How long does it take to AES encrypt/ decrypt a 150GB BAM file? With the advent of policies like GDPR I'm worried that files in our European data management systems would have to encrypt genomes at the file level. Really worried that this will ruin our day-to-day usability for research. I've heard ...
gdpr hipaa encryption written 14 months ago by syntax30 • updated 12 months ago by Biostar ♦♦ 20
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Blog: Clarifying the concept of clinical annotation vs bioinformatic annotation
... *The Concept of Annotation in Comparison to Assessment* === Working at a company with both clinical and bioinformatic leaders, there is confusion about the concept of “annotation.” I believe that this stems from the fact that annotation can mean one thing in a clinical context and something comple ...
annotation reference data variant blog written 16 months ago by syntax30 • updated 16 months ago by Devon Ryan88k

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