Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
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Google Scholar Page
Last seen:
17 hours ago
Joined:
8 years, 11 months ago
Email:
l******@gmail.com

I am a bioinformatics software developer known mostly for my posts on big-ass serversdamn microarray papers, and the reproducible research guilt trip, as well as my review of pipeline frameworks. I have worked in virology, crop genomics, and on various pediatric diseases as a programmer, analyst, and architect. I'm currently a PhD student at Drexel.

Posts by Jeremy Leipzig

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Comment: C: why GATK makes things more complicated ?
... Not sure how much NIH money went toward GATK, definitely >$1M http://grantome.com/grant/NIH/U01-HG006569-01 but maybe not for the initial development ...
written 6 days ago by Jeremy Leipzig18k
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Comment: C: Fields with biggest demand for bioinformatics?
... I would say it's probably easier to find a job if you sell yourself as a bioinformatics engineer rather than a bioinformatics scientist - i.e. HPC, workflows, cloud, etc. Often the salary structure is better on that side as well. ...
written 27 days ago by Jeremy Leipzig18k
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Comment: C: variant calling in mitochondria using whole genome sequencing
... possibly. you can set --ploidy in GATK to 100 if you want to drop the assumption of diploid genomes ...
written 8 weeks ago by Jeremy Leipzig18k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... Once again I'm not sure we have to talk about this theoretically - most cores have at least some cloud component, including the University of Chicago. Some are 50/50 hybrids. Others use it by default. I was just surprised that the word "cloud" is not in a 2018 bfx sysadmin job ad, even as a wishlist ...
written 9 weeks ago by Jeremy Leipzig18k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... "on-demand rent of virtualized computing infrastructure". Even 5 years ago the cloud was not a particularly friendly or cheap place to do scientific computing, but things are so different now. ...
written 9 weeks ago by Jeremy Leipzig18k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... The tension I am sensing between these groups is giving me a headache and I don't even work there. ...
written 9 weeks ago by Jeremy Leipzig18k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... That sounds like a propositional fallacy - people are already storing patient data in S3 in the present day. I don't think these are insurmountable issues. ...
written 9 weeks ago by Jeremy Leipzig18k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... I don't normally threadcrap on job posts but it seems kind of crazy to advertise an HPC job with no cloud computing component. Do they really think bioinformatics will stay on bare metal machines? Isn't this Robert Grossman's group? ...
written 9 weeks ago by Jeremy Leipzig18k
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Comment: C: Cutadapt Or Fastx Clipper
... added recent entries trimmomatic (2014) and fastp (2018) ...
written 11 weeks ago by Jeremy Leipzig18k
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Answer: A: help identifying bioinformatics operations tools
... > Databasing of Patients, Samples, NGS Experiments, Bioinformatics > Applications, Analyses Results, or more yeah TransMart I2B2 > Comprenhensive RESTful API with documentation http://intermine.org ? > NGS Assets Management (Permissions, Storage, Tracking) sounds LIMS-y > Automa ...
written 12 weeks ago by Jeremy Leipzig18k

Latest awards to Jeremy Leipzig

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Great Question 6 weeks ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Popular Question 5 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 5 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 6 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Student 6 months ago, asked a question with at least 3 up-votes. For What are the best examples of sample naming conventions?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Epic Question 8 months ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp
Popular Question 9 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Appreciated 9 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 10 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Appreciated 10 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 11 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format

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