Jeff Jasper

Utah's premiere event for the life sciences industry, the #BioHiveSummit (previously known as the Utah Life Sciences Summit) is coming virtually November 12. Save the date. More details coming soon. #bioutah #biohive #utahlifesciences bioutah.org

The discussion about SARS-CoV-2 origins has become a toxic quagmire of false equivalence. Maybe you heard that evidence for lab leak has increased, but not for zoonotic origin? That's not true. Dr. @stgoldst & I argue the evidence still points to nature. washingtonpost.com/outlook/virus-…

10/ Contact your Senators and urge them to vote for the Wyden-Lummis-Toomey amendment and vote NO on the Warner-Portman amendment. Let’s keep crypto alive and thriving, we’re just getting started. p2a.co/y19AJ6V

Launching a new dashboard to track local news reports and state press releases on how many vaccine doses will be allocated to each state, since there seems to be no public federal effort. Browse each state's allocations and a map of doses per capita. public.tableau.com/views/COVID-19…

Republicans like to show off a map 🗺 of the country being red, but it’s mostly empty space. Land doesn’t vote. People do. #ThursdayThoughts #ElectionResults2020 pic.twitter.com/6QKgWJzwjZ

For mid Nov., I am writing a grant to support improved algorithms and functionality for bedtools. I would be eager to know of desired new functionality, file support, algorithms, or things that you cannot do easily but wish you could. User feedback is incredibly valuable. Pls. RT

@0_minyaaa Wholeheartedly agree for gene expression but would also say that RT-PCR is still necessary to confirm isoform-level analysis, esp when comparing isoform functionality within same gene. Leading RNA-Seq algorithms work for most isoform disambiguation but lots of edge cases.

Oops, being asked to confirm #RNAseq results with #qRT-PCR again by a reviewer. Although I have, um (check notes), EIGHT biological replicates per developmental stage. 😬

NR: FFPE is the most commonly used preservation method, and today we are introducing FFPE enablement. Using a modified Visium protocol we are able to recover data that correlates between FFPE and Fresh Frozen #AGBT20

Took a few years but work from grad school was recently published and made news at Duke. New Approach to Shutting Down Breast Cancer Recurrence Shows Promise in Mice | Duke Health: corporate.dukehealth.org/news-listing/n…

Time-restricted eating (6hr window) lowered mean blood glucose levels, increased ketones, lowered evening cortisol, elevated evening BDNF, and increased the levels of an autophagy gene by 22% compared to eating same calories within a 12hr window (humans). ncbi.nlm.nih.gov/pmc/articles/P…

Presented by @WeWork: Here's why North Carolina is one of the most business-friendly states in the country. 53eig.ht/2Y5uasr

Amazing

@loganjeverett Imagine the opposite world where the installed version is practically useless because it is at least 5 years out of date. Living on the bleeding edge is painful but a no update policy is equally absurd. Conda environments or modules is a nice balance.

TFW your SysAd upgrades to a new version of R without asking and all your packages need to be reinstalled.

@nextflowio Either is perfectly fine but please keep the behavior where it throws a warning —and not die— when “-resume” is used on a first run. As a user I would hate to have to know the state of every job before I execute. It is a matter of convenience.

Should -resume⏯️ be the default when launching a Nextflow pipeline?

Mark your calendars April 8-10 for #MAQC2020 in Cary, North Carolina. Immediately before our conference is #MCBIOS2020 at the same venue. Stay tuned for details!

@AviMaayan @MaayanLab @BD2KLINCSDCIC @IcahnMountSinai @IcahnInstitute I’ve used enrichr and recommend to many. Great tool! Now work in a commercial lab but licensing is not clear to me. License for non-academics?

#Enrichr just reached a new milestone of 20,000,000 gene-set query submissions!!! Give it a try at amp.pharm.mssm.edu/Enrichr congrats to @MaayanLab @BD2KLINCSDCIC @IcahnMountSinai @IcahnInstitute

Nice to see the 3x speed up for bwamem2! Should also mention @sentieon equivalent of bwamem which is also 2-3x speed up based on our comparisons.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies biorxiv.org/content/10.110… Code github.com/bioinform/soma… Data sites.google.com/view/seqc2/hom…

@nextflowio @nf_core @QBIC_tue Thanks for the links! I should mention that I’m not focusing on pipelines. Trying to see what frameworks, dashboards, APIs, and the like we’re built on top of nextflow for ease of operations at scale.

@_jasper1918 @nf_core @QBIC_tue Other (public) relevant is github.com/IARCbioinfo/IA…. Then you can also check github.com/IARCbioinfo/IA…. Finally github.com/search?q=exten…

Does anyone have a semi-comprehensive list of integrating software or projects that leverage @nextflowio ? So far I know of @nf_core @QBIC_tue #flowcraft #innuendo #pipeliner